popup window is not opening up in igv.js beta version for gwas track

[selimkal]

Hi,

I have been using igv.js to display some eqtl data in the browser, using format: 'gtexGWAS', featureType: 'gwas'

for track configuration. For this, I have been using the following js file: https://igv.org/web/beta/igv-beta.js

Until recently, it was working fine. But, lately, the popup window that should open when clicked on a specific eqtl data (drawn as a circle) is not working.

(I tried switching the js file to regular web release, but that doesn't seem to support gtexGWAS format yet.)

Any suggestions to resolve this?

Thanks.

[jrobinso]

Hi,

Thanks for the report, but which web release did you use? The gtex portal itself (https://www.gtexportal.org/home/) uses release 1.0.1. The latest release is 1.0.7.

Could you attach your igv.js configuration the html page or a snippet of it)?

On Tue, Apr 4, 2017 at 9:05 AM, selimkal notifications@github.com wrote:

Hi,

I have been using igv.js to display some eqtl data in the browser, using format: 'gtexGWAS', featureType: 'gwas'

for track configuration. For this, I have been using the following js file: https://igv.org/web/beta/igv-beta.js

Until recently, it was working fine. But, lately, the popup window that should open when clicked on a specific eqtl data (drawn as a circle) is not working.

(I tried switching the js file to regular web release, but that doesn't seem to support gtexGWAS format yet.)

Any suggestions to resolve this?

Thanks.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/385, or mute the thread https://github.com/notifications/unsubscribe-auth/AA49HBwwOTfHAGr11WGodMDgJrM1UZrQks5rsmpngaJpZM4MzFNa .

[selimkal]

Hi Jim,

The igv.js import in my html is done by:

Please let me know if you need/mean other/additional snippet.

I have tried the same web release (1.0.1) gtex portal uses, as well as release 1.0.7, but neither would support eqtl visualization/track in my case. I am not sure, but I have two quick theories about why that might be so:

1- I use flat files, contrary to gtex portal which uses web service to transfer data, to generate eqtl track. Web release (1.0.1 - 1.0.7) may be supporting only the web service approach. 2- gtex portal page may have included additional customized scripts to support eqtl track with igv.js web release 1.0.1.

Regardless of the above, the beta version was (and is still, except for the bug) supporting eqtl track quite nicely, for visualizing flat file data which I currently use. The only issue is the problem with the popup window that has happened only recently.

Hope this explains a bit further. Should you need further information, please let me know.

Thanks!

On Tue, Apr 4, 2017 at 1:51 PM, Jim Robinson notifications@github.com wrote:

Hi,

Thanks for the report, but which web release did you use? The gtex portal itself (https://www.gtexportal.org/home/) uses release 1.0.1. The latest release is 1.0.7.

Could you attach your igv.js configuration the html page or a snippet of it)?

On Tue, Apr 4, 2017 at 9:05 AM, selimkal notifications@github.com wrote:

Hi,

I have been using igv.js to display some eqtl data in the browser, using format: 'gtexGWAS', featureType: 'gwas'

for track configuration. For this, I have been using the following js file: https://igv.org/web/beta/igv-beta.js

Until recently, it was working fine. But, lately, the popup window that should open when clicked on a specific eqtl data (drawn as a circle) is not working.

(I tried switching the js file to regular web release, but that doesn't seem to support gtexGWAS format yet.)

Any suggestions to resolve this?

Thanks.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/385, or mute the thread https://github.com/notifications/unsubscribe-auth/ AA49HBwwOTfHAGr11WGodMDgJrM1UZrQks5rsmpngaJpZM4MzFNa .

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[jrobinso]

OK, that is helpful. Its a bit fortunate this is working at all for you, the flat eqtl files originally supported the gtex portal (thus gtex in the name). However the portal now uses a webservice, as you note, and the eqtl flat files are not supported or tested anymore. I assume you discovered this format from browsing the source code. Could you provide a small test file, and also a sample web page or track config javascript snippet that uses it?

[selimkal]

Hi Jim,

I see, good to know about the flat-files/web-service support. And yes, I had seen the usage of flat files for eqtl data in one of the (rather old) test pages I believe.

Attached please find a sample eqtl flat file (please note that some columns are simply placeholders, added just to make it work in browser).

And here is the loadTrack snippet I use in the html:

igv.browser.loadTrack({ url: './data/tes-cis-eqtl.txt', name: 'test', format: 'gtexGWAS', featureType: 'gwas', colorScale: { thresholds: [], colors:['rgb(122,179,23)'] },

                                maxLogP: 16,
                                height: 150,
                                label: 'Test'});
        }

Hope this would help.

Thanks!

On Thu, Apr 6, 2017 at 11:38 AM, Jim Robinson notifications@github.com wrote:

OK, that is helpful. Its a bit fortunate this is working at all for you, the flat eqtl files originally supported the gtex portal (thus gtex in the name). However the portal now uses a webservice, as you note, and the eqtl flat files are not supported or tested anymore. I supposed you discovered this format from browsing the source code. Could you provide a small test file, and also a sample web page or track config javascript snippet that uses it?

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SNP_Chr SNP_Pos_hg19 Transcript_GeneSymbol 1:243544827 Rs_ID P-val phen Gene 1 28225114 RPA2 1:243544827 rs1000431 1.45E-18 phen RPA2 4 1324346 CRIPAK 1:243544827 rs10012416 1.43E-14 phen CRIPAK 4 84167984 HPSE 1:243544827 rs10014278 3.19E-05 phen HPSE 4 2862190 MFSD10 1:243544827 rs10026792 7.53E-05 phen MFSD10 4 88292147 HSD17B11 1:243544827 rs10034537 0.000147690179652976 phen HSD17B11 5 176484984 MXD3 1:243544827 rs10035183 0.000101460925956596 phen MXD3 5 95990869 CAST 1:243544827 rs10039522 6.90E-08 phen CAST 12 129625269 SLC15A4 1:243544827 rs10047656 0.00024678557764908 phen SLC15A4 5 176735187 RAB24 1:243544827 rs10051822 0.000109593885762883 phen RAB24 5 35512003 BRIX1 1:243544827 rs10065345 0.000108780888918509 phen BRIX1 5 75803002 PDE8B 1:243544827 rs10066611 0.000136411934082815 phen PDE8B 5 179050918 HNRNPH1 1:243544827 rs10066669 9.47E-08 phen HNRNPH1 5 150123251 C5orf62 1:243544827 rs10068228 6.19E-05 phen C5orf62 5 147547917 FBXO38 1:243544827 rs10068916 2.03E-06 phen FBXO38 5 95990057 CAST 1:243544827 rs10075736 6.04E-13 phen CAST 15 90799802 NGRN 1:243544827 rs10083710 0.000151023197346242 phen NGRN 8 131420688 ASAP1 1:243544827 rs10086773 0.000129773412059186 phen ASAP1 8 28909523 HMBOX1 1:243544827 rs10088428 8.92E-10 phen HMBOX1 8 41234902 GOLGA7 1:243544827 rs10088901 5.14E-05 phen GOLGA7 8 3165777 ??? 1:243544827 rs10091831 0.000122948939352581 phen ??? 5 149492119 DCTN4 1:243544827 rs1009424 0.00023937918604321 phen DCTN4 8 23324877 ENTPD4 1:243544827 rs10094683 1.09E-10 phen ENTPD4 19 48702219 CARD8 1:243544827 rs1010089 7.17E-19 phen CARD8 8 6793006 DEFA4 1:243544827 rs10103091 6.89E-06 phen DEFA4 8 145004944 PLEC1 1:243544827 rs10107388 5.85E-06 phen PLEC1 8 81791762 TPD52 1:243544827 rs10112204 0.000159993599405168 phen TPD52 9 103065265 INVS 1:243544827 rs10124893 2.83E-06 phen INVS 14 21274036 RPGRIP1 1:243544827 rs10131805 6.67E-05 phen RPGRIP1 14 93148543 BTBD7 1:243544827 rs10139162 2.58E-05 phen BTBD7 14 93693604 UBR7 1:243544827 rs10144530 2.83E-05 phen UBR7 14 24899194 KHNYN 1:243544827 rs10146759 5.31E-13 phen KHNYN 14 100838007 SLC25A29 1:243544827 rs10149239 9.30E-14 phen SLC25A29 14 78380965 ADCK1 1:243544827 rs10150472 5.44E-12 phen ADCK1 9 96345328 FAM120AOS 1:243544827 rs10156602 0.000148145375061101 phen FAM120AOS 11 65667149 MUS81 1:243544827 rs10160792 3.08E-06 phen MUS81 18 9542084 PPP4R1 1:243544827 rs10163801 1.66E-05 phen PPP4R1 12 108949966 ISCU 1:243544827 rs1016881 9.13E-14 phen ISCU 2 30449594 LBH 1:243544827 rs10175798 7.77E-08 phen LBH 2 48994107 CCDC128 1:243544827 rs10176937 0.000119569297541119 phen CCDC128 2 85524876 TGOLN2 1:243544827 rs10178604 9.69E-05 phen TGOLN2 2 88949205 RPIA 1:243544827 rs10178815 0.000182640507008978 phen RPIA 2 160427646 BAZ2B 1:243544827 rs10202187 3.79E-13 phen BAZ2B 2 201806597 CASP8 1:243544827 rs10207973 6.55E-05 phen CASP8 2 100075804 REV1 1:243544827 rs10207981 1.27E-05 phen REV1 12 26569724 SSPN 1:243544827 rs1021296 0.000126647925312339 phen SSPN 4 88291760 HSD17B11 1:243544827 rs10213098 0.000260699941189299 phen HSD17B11 4 4864276 LYAR 1:243544827 rs10213148 4.81E-05 phen LYAR 4 175632850 GPM6A 1:243544827 rs10213402 0.000157278996774258 phen GPM6A 7 128599397 IRF5 1:243544827 rs10229001 6.36E-32 phen IRF5 7 128599397 IRF5 1:243544827 rs10229001 7.93E-15 phen IRF5 7 97785669 TECPR1 1:243544827 rs10243469 1.81E-05 phen TECPR1 7 140936088 KIAA1147 1:243544827 rs1024722 0.000197813722609637 phen KIAA1147 7 102022586 LRWD1 1:243544827 rs10249581 6.46E-14 phen LRWD1 7 44584551 ??? 1:243544827 rs10260606 5.52E-05 phen ??? 11 3865786 TRIM68 1:243544827 rs1026231 5.28E-05 phen TRIM68 7 38636891 GPR141 1:243544827 rs10263645 0.00020568202311997 phen GPR141 7 30731993 FAM188B 1:243544827 rs10271601 4.81E-05 phen FAM188B 8 144107977 LY6E 1:243544827 rs10283236 1.05E-08 phen LY6E 9 125157198 PTGS1 1:243544827 rs10306194 6.51E-05 phen PTGS1 4 102223386 FLJ20021 1:243544827 rs1031034 5.81E-13 phen FLJ20021 8 9040858 PPP1R3B 1:243544827 rs1038248 0.000244494555920015 phen PPP1R3B 5 73927752 ENC1 1:243544827 rs1039320 1.66E-32 phen ENC1 5 73927752 HEXB 1:243544827 rs1039320 5.94E-06 phen HEXB 1 203156080 MYBPH 1:243544827 rs10399931 1.68E-17 phen MYBPH 6 111902079 TRAF3IP2 1:243544827 rs1040382 1.48E-08 phen TRAF3IP2 19 40777133 PLD3 1:243544827 rs10405207 0.000143339270974138 phen PLD3 19 45011727 ZNF234 1:243544827 rs10408058 2.87E-05 phen ZNF234 19 20782523 ZNF431 1:243544827 rs10411545 2.02E-05 phen ZNF431 19 43202770 LYPD3 1:243544827 rs10412221 5.34E-05 phen LYPD3 19 2575186 REXO1 1:243544827 rs10419362 0.000118265964613741 phen REXO1 19 42125660 CEACAM4 1:243544827 rs1041994 1.00E-19 phen CEACAM4 19 19383537 KIAA0892 1:243544827 rs10419998 9.62E-16 phen KIAA0892 19 49390878 DHDH 1:243544827 rs10423931 9.19E-05 phen DHDH 5 137902339 PAIP2 1:243544827 rs1042665 3.39E-05 phen PAIP2 6 43753212 ZNF318 1:243544827 rs10434 0.000138460768708134 phen ZNF318 22 42981678 NDUFA6 1:243544827 rs1043606 0.000176163164189338 phen NDUFA6 19 15708779 CYP4F3 1:243544827 rs10439166 0.000157463896249393 phen CYP4F3 2 203055522 CASP8 1:243544827 rs10445793 6.04E-05 phen CASP8 8 17917428 ASAH1 1:243544827 rs10448131 5.10E-11 phen ASAH1 5 132752323 SKP1 1:243544827 rs10452539 0.000283362981110264 phen SKP1 8 142200467 DENND3 1:243544827 rs1045303 2.54E-07 phen DENND3 11 20265876 ??? 1:243544827 rs10458881 0.000246625051048321 phen ??? 19 1095514 GPX4 1:243544827 rs1046040 5.99E-07 phen GPX4 1 22443887 HSPC157 1:243544827 rs1046310 9.80E-11 phen HSPC157 2 74699778 MRPL53 1:243544827 rs1047911 1.98E-05 phen MRPL53 7 73108924 WBSCR22 1:243544827 rs10479665 1.46E-11 phen WBSCR22 1 182542851 RNASEL 1:243544827 rs1048260 3.49E-05 phen RNASEL 6 38979441 C6orf64 1:243544827 rs10484850 7.00E-05 phen C6orf64 10 112053599 SMNDC1 1:243544827 rs1050755 9.51E-07 phen SMNDC1 7 100782460 GNB2 1:243544827 rs1050955 9.57E-05 phen GNB2 5 51955408 PELO 1:243544827 rs10512980 0.000151368076302287 phen PELO 9 111881856 C9orf6 1:243544827 rs1051474 1.18E-05 phen C9orf6 3 127391378 ABTB1 1:243544827 rs1056235 2.03E-07 phen ABTB1 20 7962128 TMX4 1:243544827 rs1058007 4.53E-09 phen TMX4 13 52319678 DHRS12 1:243544827 rs1060562 2.13E-05 phen DHRS12 10 100189138 HPS1 1:243544827 rs1061135 0.000247364364585373 phen HPS1 19 1086211 POLR2E 1:243544827 rs1061233 0.000265642859180972 phen POLR2E 9 135764081 C9orf9 1:243544827 rs1062218 0.000120073510332433 phen C9orf9 7 87835469 SRI 1:243544827 rs1063964 1.59E-05 phen SRI 15 45981317 SQRDL 1:243544827 rs10643 1.63E-08 phen SQRDL 6 32546615 NCR3 1:243544827 rs1064717 8.69E-05 phen NCR3 16 1839134 NME3 1:243544827 rs1065666 5.96E-05 phen NME3 12 1947193 ADIPOR2 1:243544827 rs10735004 2.84E-05 phen ADIPOR2 9 75991893 ANXA1 1:243544827 rs10735622 3.68E-10 phen ANXA1 12 41800488 PPHLN1 1:243544827 rs10735993 0.000262163983886547 phen PPHLN1 14 94353093 MOAP1 1:243544827 rs1073778 6.25E-05 phen MOAP1 9 124021025 GSN 1:243544827 rs10739593 1.04E-07 phen GSN 12 124231355 ATP6V0A2 1:243544827 rs10744161 1.21E-05 phen ATP6V0A2 12 97871380 NEDD1 1:243544827 rs10745798 5.54E-05 phen NEDD1 1 213050209 LQK1 1:243544827 rs10746439 2.50E-16 phen LQK1 12 56077418 BAZ2A 1:243544827 rs10747759 0.000113075797205558 phen BAZ2A 10 101283330 BLOC1S2 1:243544827 rs10748781 8.55E-05 phen BLOC1S2 1 168166616 TIPRL 1:243544827 rs10753766 2.62E-08 phen TIPRL 8 21762915 XPO7 1:243544827 rs1075417 1.88E-05 phen XPO7 9 35776190 GBA2 1:243544827 rs10758322 3.28E-06 phen GBA2 9 104623299 RNF20 1:243544827 rs10760813 5.50E-05 phen RNF20 10 71040106 HNRPH3 1:243544827 rs10762273 0.000163874357199423 phen HNRPH3 11 3914033 STIM1 1:243544827 rs10767685 1.10E-06 phen STIM1 6 36348689 ETV7 1:243544827 rs1076928 6.03E-10 phen ETV7 12 10215582 CLEC9A 1:243544827 rs10772230 9.05E-08 phen CLEC9A 12 10492728 KLRC3 1:243544827 rs10772261 0.000101338522546955 phen KLRC3 12 6242259 VWF 1:243544827 rs10774396 3.75E-14 phen VWF 15 58723426 AQP9 1:243544827 rs1077835 0.000257243207454436 phen AQP9 12 109133588 CORO1C 1:243544827 rs10778656 1.05E-09 phen CORO1C 9 78242109 PCSK5 1:243544827 rs10781300 3.77E-07 phen PCSK5 12 53847473 C12orf10 1:243544827 rs10783580 3.39E-06 phen C12orf10 11 65363865 KAT5 1:243544827 rs10791819 0.000200902878356274 phen KAT5 11 65363865 MAP3K11 1:243544827 rs10791819 3.62E-08 phen MAP3K11 10 7319541 PRKCQ 1:243544827 rs10795539 5.89E-05 phen PRKCQ 1 156735422 C1orf66 1:243544827 rs10796965 0.000149363309105606 phen C1orf66 1 160497984 CD84 1:243544827 rs10797073 1.32E-05 phen CD84 1 182373498 GLUL 1:243544827 rs10797773 6.03E-05 phen GLUL 1 185394834 IVNS1ABP 1:243544827 rs10798014 0.000108398870819528 phen IVNS1ABP 1 33941028 S100PBP 1:243544827 rs10798954 0.000116535220277128 phen S100PBP 1 200508928 CSRP1 1:243544827 rs10800707 0.000278059142334148 phen CSRP1 1 236311886 GPR137B 1:243544827 rs10802285 0.000182938541798671 phen GPR137B 1 236771229 LGALS8 1:243544827 rs10802552 1.30E-07 phen LGALS8 1 15278473 KIAA1026 1:243544827 rs10803327 2.27E-14 phen KIAA1026 7 151633265 GALNT11 1:243544827 rs10807990 2.53E-07 phen GALNT11 7 107552088 BCAP29 1:243544827 rs10808155 7.55E-05 phen BCAP29 1 93854688 DR1 1:243544827 rs1081521 1.81E-10 phen DR1 9 123572038 LOC253039 1:243544827 rs10818476 7.86E-26 phen LOC253039 9 125002275 RBM18 1:243544827 rs10818655 9.36E-05 phen RBM18 10 72064976 TYSND1 1:243544827 rs10823515 9.17E-06 phen TYSND1 10 75464853 SEC24C 1:243544827 rs10824028 4.82E-05 phen SEC24C 11 93370692 C11orf54 1:243544827 rs10831080 0.000202388805446248 phen C11orf54 11 93421782 SNORA25 1:243544827 rs10831093 2.13E-11 phen SNORA25 11 2927670 SLC22A18AS 1:243544827 rs10832888 0.00027600042102939 phen SLC22A18AS 11 7606498 PPFIBP2 1:243544827 rs10839816 2.53E-09 phen PPFIBP2 11 8736695 TRIM66 1:243544827 rs10840114 1.88E-09 phen TRIM66 12 9935825 GABARAPL1 1:243544827 rs10844782 0.000133040249207915 phen GABARAPL1 12 7900184 CLEC4C 1:243544827 rs10845821 2.31E-35 phen CLEC4C 12 131295828 STX2 1:243544827 rs10848208 3.07E-09 phen STX2 12 6412036 PTMS 1:243544827 rs10849438 0.000233577606674428 phen PTMS 12 6654050 HOM-TES-103 1:243544827 rs10849488 3.33E-11 phen HOM-TES-103 15 63100467 RAB8B 1:243544827 rs10851718 7.08E-05 phen RAB8B 1 111733724 CEPT1 1:243544827 rs10857859 8.63E-05 phen CEPT1 9 137857863 FCN1 1:243544827 rs10858304 1.28E-09 phen FCN1 12 92956190 MRPL42 1:243544827 rs10859340 0.000270303041652793 phen MRPL42 12 102293288 DRAM1 1:243544827 rs10860815 5.86E-09 phen DRAM1 1 219260673 LYPLAL1 1:243544827 rs10863423 4.68E-09 phen LYPLAL1 3 49858142 UBA7 1:243544827 rs10865958 8.80E-18 phen UBA7 8 23468924 NKX3-1 1:243544827 rs10866831 1.36E-21 phen NKX3-1 9 140534584 ARRDC1 1:243544827 rs10867035 5.35E-05 phen ARRDC1 9 72313481 PTAR1 1:243544827 rs10867922 1.26E-08 phen PTAR1 9 140006491 MAN1B1 1:243544827 rs10870180 7.00E-09 phen MAN1B1 14 23217371 RBM23 1:243544827 rs10873040 1.57E-05 phen RBM23 12 49012011 C12orf41 1:243544827 rs10875848 1.01E-06 phen C12orf41 12 56050706 DGKA 1:243544827 rs10876844 0.000261124760584804 phen DGKA 3 4114156 TRNT1 1:243544827 rs1087823 5.52E-05 phen TRNT1 12 66872341 HMGA2 1:243544827 rs10878433 0.000158212696704638 phen HMGA2 12 46595290 SLC38A1 1:243544827 rs10880935 0.000226174929538926 phen SLC38A1 10 104973061 C10orf32 1:243544827 rs10883848 6.45E-06 phen C10orf32 1 151068637 CDC42SE1 1:243544827 rs10888404 1.04E-05 phen CDC42SE1 1 153171148 SPRR2D 1:243544827 rs10888535 0.000249047422175854 phen SPRR2D 11 126425577 ST3GAL4 1:243544827 rs10893539 3.55E-05 phen ST3GAL4 11 129698856 TMEM45B 1:243544827 rs10894147 1.76E-18 phen TMEM45B 11 72700779 ATG16L2 1:243544827 rs10898894 0.000204941336870698 phen ATG16L2 11 76600932 PHCA 1:243544827 rs10899303 8.40E-11 phen PHCA 11 960641 RIC8A 1:243544827 rs10902251 1.57E-05 phen RIC8A 1 26666196 AIM1L 1:243544827 rs10902740 2.46E-05 phen AIM1L 10 5541181 RBM17 1:243544827 rs10904516 2.13E-05 phen RBM17 1 154710904 HAX1 1:243544827 rs10908429 7.85E-05 phen HAX1 1 161008535 TSTD1 1:243544827 rs10908821 3.87E-18 phen TSTD1 1 161008535 TSTD1 1:243544827 rs10908821 7.19E-06 phen TSTD1 1 181493767 CACNA1E 1:243544827 rs10910948 8.34E-05 phen CACNA1E 1 183489203 SMG7 1:243544827 rs10911353 7.15E-17 phen SMG7 3 126212567 ZXDC 1:243544827 rs1091553 2.37E-08 phen ZXDC 1 24085063 FUCA1 1:243544827 rs10917423 5.61E-10 phen FUCA1 1 19756869 CAPZB 1:243544827 rs10917449 2.77E-06 phen CAPZB 16 10829280 TXNDC11 1:243544827 rs1091849 0.000186756450729357 phen TXNDC11 2 15737268 DDX1 1:243544827 rs10929377 2.24E-19 phen DDX1 2 10558066 HPCAL1 1:243544827 rs10929663 9.46E-07 phen HPCAL1 6 89569254 RNGTT 1:243544827 rs10944411 2.49E-07 phen RNGTT 7 6541015 AIMP2 1:243544827 rs10951985 0.000137026687318167 phen AIMP2 8 124782340 MTSS1 1:243544827 rs10956148 0.000130050395073069 phen MTSS1 8 38052482 LSM1 1:243544827 rs10958541 2.46E-20 phen LSM1 8 39798341 IDO1 1:243544827 rs10958575 7.76E-06 phen IDO1 9 34151280 NUDT2 1:243544827 rs10971956 1.98E-13 phen NUDT2 9 5433404 JAK2 1:243544827 rs10975114 5.85E-05 phen JAK2 9 100736718 ??? 1:243544827 rs10984599 9.83E-05 phen ??? 9 130611523 C9orf114 1:243544827 rs10987756 0.000171917748382816 phen C9orf114 9 133014623 LOC158301 1:243544827 rs10988658 0.000132175255094301 phen LOC158301 9 95551617 BICD2 1:243544827 rs10992469 1.55E-07 phen BICD2 9 97058302 HIATL1 1:243544827 rs10993151 2.23E-20 phen HIATL1 10 51563993 TIMM23 1:243544827 rs10994675 6.96E-07 phen TIMM23 10 69602892 SIRT1 1:243544827 rs10997828 7.43E-21 phen SIRT1 10 70386834 SUPV3L1 1:243544827 rs10998342 0.000189582196576523 phen SUPV3L1 10 71043781 HNRNPH3 1:243544827 rs10998696 0.00013570880175954 phen HNRNPH3 10 72174390 EIF4EBP2 1:243544827 rs10999323 1.44E-05 phen EIF4EBP2 10 52357891 SGMS1 1:243544827 rs11006259 9.81E-05 phen SGMS1 10 20414564 PLXDC2 1:243544827 rs11011813 0.000192000641223335 phen PLXDC2 10 26706338 YME1L1 1:243544827 rs11015094 0.000269542672528715 phen YME1L1 10 129892160 PTPRE 1:243544827 rs11016068 0.000126519194155101 phen PTPRE 11 29781464 C11orf46 1:243544827 rs11030799 6.74E-05 phen C11orf46 11 32459923 EIF3M 1:243544827 rs11031783 0.000183477239207002 phen EIF3M 11 44723871 CD82 1:243544827 rs11038116 1.44E-05 phen CD82 12 22666996 KIAA0528 1:243544827 rs11046453 0.000102487309033307 phen KIAA0528 12 25051596 BCAT1 1:243544827 rs11047695 5.97E-12 phen BCAT1 4 185304463 IRF2 1:243544827 rs1105207 0.000177850007418945 phen IRF2 1 2141985 C1orf86 1:243544827 rs1105269 2.15E-07 phen C1orf86 12 10283711 CLEC7A 1:243544827 rs11053624 2.10E-06 phen CLEC7A 12 7904111 CLEC4C 1:243544827 rs11055602 5.35E-29 phen CLEC4C 12 123770362 CDK2AP1 1:243544827 rs11057242 1.85E-16 phen CDK2AP1 12 123219785 DENR 1:243544827 rs11059650 1.47E-05 phen DENR 12 6241707 CD9 1:243544827 rs11064041 4.15E-12 phen CD9 12 6705937 NOP2 1:243544827 rs11064275 0.000182335686654493 phen NOP2 13 111172407 RAB20 1:243544827 rs11069851 9.42E-08 phen RAB20 16 25039449 ARHGAP17 1:243544827 rs11074668 9.16E-13 phen ARHGAP17 17 18664378 FLII 1:243544827 rs11078420 1.94E-05 phen FLII 17 3820239 P2RX1 1:243544827 rs11078476 7.12E-24 phen P2RX1 17 40545770 VAT1 1:243544827 rs11079043 9.76E-05 phen VAT1 18 44659001 HDHD2 1:243544827 rs11082563 0.000147466205368872 phen HDHD2 19 3735215 EEF2 1:243544827 rs11085038 0.000173248314549518 phen EEF2 19 9546460 ZNF266 1:243544827 rs11086035 1.17E-11 phen ZNF266 19 9546460 ZNF266 1:243544827 rs11086035 5.88E-21 phen ZNF266 14 20849002 FLJ10357 1:243544827 rs1108614 0.000228205532379093 phen FLJ10357 21 19070092 C21orf91 1:243544827 rs11088649 5.14E-05 phen C21orf91 4 37375277 TBC1D1 1:243544827 rs11096872 6.04E-05 phen TBC1D1 4 100744401 DAPP1 1:243544827 rs11097677 5.13E-05 phen DAPP1 4 159857539 RAPGEF2 1:243544827 rs11100203 1.13E-08 phen RAPGEF2 1 111427656 KCND3 1:243544827 rs11102172 0.000125172667347624 phen KCND3 9 138980277 NACC2 1:243544827 rs11103323 1.56E-07 phen NACC2 12 104192793 NT5DC3 1:243544827 rs11111790 2.21E-05 phen NT5DC3 1 219280033 LYPLAL1 1:243544827 rs11118215 3.93E-08 phen LYPLAL1 1 209938987 TRAF3IP3 1:243544827 rs11119339 9.68E-14 phen TRAF3IP3 1 212955231 NSL1 1:243544827 rs11120025 1.68E-07 phen NSL1 1 10455148 KIF1B 1:243544827 rs11121559 2.29E-07 phen KIF1B 1 231111477 TTC13 1:243544827 rs11122172 4.52E-17 phen TTC13 1 231111477 TTC13 1:243544827 rs11122172 5.20E-15 phen TTC13 2 99884546 MITD1 1:243544827 rs11123777 7.87E-05 phen MITD1 2 3471146 TTC15 1:243544827 rs11127428 9.82E-12 phen TTC15 3 9836312 TADA3 1:243544827 rs11131186 0.000135748205918201 phen TADA3 13 77434603 KCTD12 1:243544827 rs1113312 5.71E-05 phen KCTD12 5 175904141 RNF44 1:243544827 rs11134977 9.98E-06 phen RNF44 9 140380376 FBXW5 1:243544827 rs11137268 4.42E-05 phen FBXW5 6 6810109 F13A1 1:243544827 rs111418267 0.000120255308965732 phen F13A1 9 71184184 PIP5K1B 1:243544827 rs11142965 5.93E-05 phen PIP5K1B 19 876882 CFD 1:243544827 rs111469573 1.24E-08 phen CFD 12 133385721 GOLGA3 1:243544827 rs11147084 4.28E-05 phen GOLGA3 17 259648 C17orf97 1:243544827 rs11150882 1.08E-29 phen C17orf97 17 259648 C17orf97 1:243544827 rs11150882 6.72E-32 phen C17orf97 15 42323272 NUSAP1 1:243544827 rs111532177 0.000245297284230151 phen NUSAP1 6 139099401 CCDC28A 1:243544827 rs11155000 3.79E-05 phen CCDC28A 1 76394910 RABGGTB 1:243544827 rs11161905 3.24E-05 phen RABGGTB 3 134834409 PPP2R3A 1:243544827 rs111621177 1.46E-05 phen PPP2R3A 12 51117593 DIP2B 1:243544827 rs11169530 8.10E-06 phen DIP2B 12 57287522 DCTN2 1:243544827 rs11172038 0.000281833966792196 phen DCTN2 16 1294883 FAM173A 1:243544827 rs111743119 6.02E-05 phen FAM173A 12 62530388 FAM19A2 1:243544827 rs11174342 0.000123227868694894 phen FAM19A2 17 76901058 TIMP2 1:243544827 rs111770145 5.35E-07 phen TIMP2 12 69175793 MDM2 1:243544827 rs11177370 1.10E-05 phen MDM2 12 69175793 SLC35E3 1:243544827 rs11177370 3.30E-09 phen SLC35E3 12 69769275 YEATS4 1:243544827 rs11177631 2.57E-10 phen YEATS4 19 2191796 GNA15 1:243544827 rs111785160 3.45E-05 phen GNA15 12 43405540 YAF2 1:243544827 rs11181845 2.00E-05 phen YAF2 12 47719326 LOC728181 1:243544827 rs11183849 0.000152601059473514 phen LOC728181 20 3052586 SPEF1 1:243544827 rs111869749 7.96E-05 phen SPEF1 8 39816912 INDO 1:243544827 rs111880438 9.26E-05 phen INDO 10 99159096 FRAT1 1:243544827 rs11189203 1.97E-09 phen FRAT1 10 99181008 FRAT2 1:243544827 rs11189214 4.80E-07 phen FRAT2 10 101185830 CHUK 1:243544827 rs11190087 0.000111001703485336 phen CHUK 10 105170649 USMG5 1:243544827 rs11191683 6.63E-43 phen USMG5 10 105245352 C10orf78 1:243544827 rs11191711 0.000190512694944968 phen C10orf78 10 112013274 ??? 1:243544827 rs11195048 0.000129987667599754 phen ??? 10 81931780 ANXA11 1:243544827 rs11201966 9.60E-09 phen ANXA11 10 89895807 ??? 1:243544827 rs11202661 0.000132855090039766 phen ??? 16 88827338 CDK10 1:243544827 rs112028717 7.20E-08 phen CDK10 10 91213935 FAS 1:243544827 rs11203134 6.61E-05 phen FAS 1 151793174 FAM63A 1:243544827 rs11204894 0.000166263169282398 phen FAM63A 1 44474802 CCDC24 1:243544827 rs11210939 1.61E-18 phen CCDC24 1 44541961 MED8 1:243544827 rs11210951 8.22E-06 phen MED8 1 48016189 CMPK1 1:243544827 rs11211551 0.000272660865474489 phen CMPK1 11 108053887 ATM 1:243544827 rs11212542 6.37E-13 phen ATM 11 86683231 ??? 1:243544827 rs112141754 3.61E-06 phen ??? 19 50047311 RCN3 1:243544827 rs112173908 3.44E-08 phen RCN3 20 60243836 OSBPL2 1:243544827 rs1122269 5.43E-05 phen OSBPL2 11 58589305 FAM111A 1:243544827 rs11229642 9.24E-06 phen FAM111A 17 46191032 SP6 1:243544827 rs112306902 8.85E-05 phen SP6 11 64046885 NUDT22 1:243544827 rs11231741 0.000188609303502628 phen NUDT22 10 35550294 CUL2 1:243544827 rs112355105 1.90E-07 phen CUL2 19 46310228 SYMPK 1:243544827 rs112400363 0.000209044895929256 phen SYMPK 2 127419105 GYPC 1:243544827 rs112403595 5.23E-07 phen GYPC 2 127419105 GYPC 1:243544827 rs112403595 5.52E-06 phen GYPC 9 134585181 RAPGEF1 1:243544827 rs11243480 2.68E-12 phen RAPGEF1 10 126323766 FAM53B 1:243544827 rs11245322 0.000239815785106628 phen FAM53B 5 176041931 B4GALT7 1:243544827 rs1124715 0.000220158407224203 phen B4GALT7 2 109042440 GCC2 1:243544827 rs112482682 0.000228421974579343 phen GCC2 10 124814481 ??? 1:243544827 rs11248371 3.21E-05 phen ??? 2 85094533 ST3GAL5 1:243544827 rs112524336 0.000254735041022514 phen ST3GAL5 10 12307894 ??? 1:243544827 rs11257655 1.27E-09 phen ??? 10 12307894 CAMK1D 1:243544827 rs11257655 8.55E-10 phen CAMK1D 10 12307894 CDC123 1:243544827 rs11257655 2.63E-07 phen CDC123 10 14534753 FAM107B 1:243544827 rs11259141 2.73E-06 phen FAM107B 17 34896877 GGNBP2 1:243544827 rs11263770 1.16E-09 phen GGNBP2 1 159976867 PIGM 1:243544827 rs11265305 0.000199657074809162 phen PIGM 16 1853335 HN1L 1:243544827 rs112690906 0.000232718015784108 phen HN1L 1 153779412 GATAD2B 1:243544827 rs1127091 4.61E-06 phen GATAD2B 19 40344366 ITPKC 1:243544827 rs112728066 0.00024888947935896 phen ITPKC 12 124559539 ??? 1:243544827 rs112745336 0.000130133078843364 phen ??? 3 183652932 ABCC5 1:243544827 rs112754234 2.89E-11 phen ABCC5 1 43443376 ELOVL1 1:243544827 rs112761111 0.000253321197068162 phen ELOVL1 11 32648203 PRRG4 1:243544827 rs112773089 1.70E-05 phen PRRG4 7 51091874 GRB10 1:243544827 rs112826922 1.80E-05 phen GRB10 17 40127060 AOC2 1:243544827 rs11296 0.000141658842773418 phen AOC2 7 100892196 CLDN15 1:243544827 rs112971669 8.58E-05 phen CLDN15 7 128755229 LOC286016 1:243544827 rs112984431 0.000157077350629057 phen LOC286016 1 33789968 PHC2 1:243544827 rs1130800 6.04E-06 phen PHC2 17 4637396 ZMYND15 1:243544827 rs1131456 2.42E-07 phen ZMYND15 4 102009720 PPP3CA 1:243544827 rs113159161 7.31E-05 phen PPP3CA 17 17145154 FLCN 1:243544827 rs113161761 4.48E-07 phen FLCN 12 7247395 C1RL 1:243544827 rs1132216 2.22E-07 phen C1RL 19 35919422 ALKBH6 1:243544827 rs113255036 6.96E-06 phen ALKBH6 6 31415150 LOC100129668 1:243544827 rs113286688 8.87E-06 phen LOC100129668 7 1133305 ZFAND2A 1:243544827 rs1133043 6.29E-08 phen ZFAND2A 1 156693135 CRABP2 1:243544827 rs1133856 6.35E-05 phen CRABP2 17 36968710 MED1 1:243544827 rs113435706 0.000245581713543445 phen MED1 16 68335392 NFATC3 1:243544827 rs11350 0.000113774081315591 phen NFATC3 6 15195682 DTNBP1 1:243544827 rs113532504 4.24E-06 phen DTNBP1 8 101765988 RNF19A 1:243544827 rs113657091 1.88E-07 phen RNF19A 3 122036822 CSTA 1:243544827 rs113686831 5.27E-06 phen CSTA 4 39804616 HIP2 1:243544827 rs113769228 6.79E-05 phen HIP2 21 34609596 IFNAR2 1:243544827 rs1137779 4.03E-06 phen IFNAR2 6 32502901 PPT2 1:243544827 rs113787140 0.000271192567216334 phen PPT2 5 142500512 ARHGAP26 1:243544827 rs113801037 9.05E-05 phen ARHGAP26 2 224832136 WDFY1 1:243544827 rs1138616 2.56E-11 phen WDFY1 12 286481 SLC6A13 1:243544827 rs113879277 8.96E-05 phen SLC6A13 6 29832919 HCG9 1:243544827 rs113959448 1.22E-19 phen HCG9 6 31438243 HCP5 1:243544827 rs114034067 0.000203962063658625 phen HCP5 6 30461085 HLA-E 1:243544827 rs114114145 2.05E-07 phen HLA-E 19 33146637 ANKRD27 1:243544827 rs114559145 4.85E-07 phen ANKRD27 6 31667028 EHMT2 1:243544827 rs114627445 2.99E-05 phen EHMT2 5 156987250 ADAM19 1:243544827 rs11465272 3.42E-05 phen ADAM19 5 11032162 ??? 1:243544827 rs114717582 0.000105806056433898 phen ??? 1 174114873 CACYBP 1:243544827 rs1147980 8.07E-05 phen CACYBP 6 31436273 C6orf48 1:243544827 rs114808309 9.83E-05 phen C6orf48 6 33298478 TAPBP 1:243544827 rs114850779 2.32E-07 phen TAPBP 9 93504263 NFIL3 1:243544827 rs1148848 0.000162858098649641 phen NFIL3 1 150930926 ARNT 1:243544827 rs114908993 3.47E-05 phen ARNT 6 13197441 PHACTR1 1:243544827 rs1150598 3.89E-15 phen PHACTR1 7 12261911 TMEM106B 1:243544827 rs11509880 2.20E-10 phen TMEM106B 7 12261911 TMEM106B 1:243544827 rs11509880 3.55E-09 phen TMEM106B 20 62374219 ZGPAT 1:243544827 rs1151626 0.000104982042228872 phen ZGPAT 6 32146657 AIF1 1:243544827 rs115186377 1.08E-07 phen AIF1 9 34162533 UBAP1 1:243544827 rs11521438 6.67E-05 phen UBAP1 14 56945549 NAT12 1:243544827 rs1152547 8.47E-05 phen NAT12 6 30990306 CLIC1 1:243544827 rs115268471 1.18E-05 phen CLIC1 6 29906044 GABBR1 1:243544827 rs115317940 3.85E-06 phen GABBR1 15 45663193 SPATA5L1 1:243544827 rs1153854 2.68E-22 phen SPATA5L1 7 154720259 LOC100132707 1:243544827 rs11543936 3.83E-06 phen LOC100132707 2 85843348 USP39 1:243544827 rs11544042 9.30E-21 phen USP39 12 6602696 VAMP1 1:243544827 rs11545055 5.27E-15 phen VAMP1 19 36246418 U2AF1L4 1:243544827 rs11549030 6.77E-10 phen U2AF1L4 6 31440415 LTA 1:243544827 rs115524885 3.08E-05 phen LTA 17 7462555 TNFSF12 1:243544827 rs11552708 3.29E-09 phen TNFSF12 6 32428397 LOC642073 1:243544827 rs115546460 1.11E-18 phen LOC642073 2 63328774 OTX1 1:243544827 rs115634863 1.50E-09 phen OTX1 7 108011965 CBLL1 1:243544827 rs1156502 0.000129549948192201 phen CBLL1 1 227189642 PSEN2 1:243544827 rs11578103 0.000108361625367859 phen PSEN2 1 161930954 B4GALT3 1:243544827 rs11579627 3.36E-05 phen B4GALT3 9 140413317 C9orf75 1:243544827 rs115803884 0.000261272532836164 phen C9orf75 1 43302515 ERMAP 1:243544827 rs11581978 8.23E-11 phen ERMAP 1 150694777 CTSS 1:243544827 rs11583636 1.02E-09 phen CTSS 1 46656964 UQCRH 1:243544827 rs11584024 2.92E-08 phen UQCRH 1 205034723 NUAK2 1:243544827 rs11588412 7.76E-06 phen NUAK2 1 78575849 USP33 1:243544827 rs11589864 0.000213276803807025 phen USP33 1 207955963 IL20 1:243544827 rs115906510 2.85E-05 phen IL20 10 27821004 RAB18 1:243544827 rs11598492 0.000266826167729231 phen RAB18 11 196944 BET1L 1:243544827 rs11604127 3.66E-06 phen BET1L 11 47725306 MYBPC3 1:243544827 rs11604825 5.44E-09 phen MYBPC3 11 75055107 ARRB1 1:243544827 rs11604864 8.58E-05 phen ARRB1 11 129718478 NFRKB 1:243544827 rs11607337 0.000272910886026419 phen NFRKB 11 62210081 B3GAT3 1:243544827 rs11607566 0.000197821988179421 phen B3GAT3 6 32638146 GPSM3 1:243544827 rs116081545 0.000160755177393362 phen GPSM3 12 29920088 TMTC1 1:243544827 rs11609828 1.74E-14 phen TMTC1 12 125494940 BRI3BP 1:243544827 rs11614174 9.08E-05 phen BRI3BP 12 33019436 C12orf35 1:243544827 rs11615313 2.51E-05 phen C12orf35 9 132613008 FNBP1 1:243544827 rs116214654 6.11E-07 phen FNBP1 14 76470655 C14orf118 1:243544827 rs11623313 0.000164176117100563 phen C14orf118 4 76826582 NAAA 1:243544827 rs116248809 4.86E-16 phen NAAA 14 21347911 RNASE2 1:243544827 rs11626267 4.14E-05 phen RNASE2 14 90968808 CCDC88C 1:243544827 rs11628344 0.000137822895800724 phen CCDC88C 14 24844054 GMPR2 1:243544827 rs11628929 0.000177690090615231 phen GMPR2 15 76608686 ETFA 1:243544827 rs11631423 2.45E-07 phen ETFA 6 31678028 LY6G5C 1:243544827 rs116336999 1.12E-13 phen LY6G5C 6 26208269 ??? 1:243544827 rs116337444 5.43E-27 phen ??? 6 31445771 MICB 1:243544827 rs116345750 2.41E-16 phen MICB 15 75088962 CSK 1:243544827 rs11635664 1.10E-09 phen CSK 15 90882643 IDH2 1:243544827 rs11638227 0.000178232994194828 phen IDH2

[selimkal]

Hi,

Any progress/feedback on this by any chance?

Thanks!

---------- Forwarded message ---------- From: Selim Kalayci skalayci@gmail.com Date: Mon, Apr 10, 2017 at 4:22 PM Subject: Re: [igvteam/igv] popup window is not opening up in igv.js beta version for gwas track (#385) To: igvteam/igv < reply@reply.github.com

Cc: igvteam/igv igv@noreply.github.com, Author author@noreply.github.com

Hi Jim,

I see, good to know about the flat-files/web-service support. And yes, I had seen the usage of flat files for eqtl data in one of the (rather old) test pages I believe.

Attached please find a sample eqtl flat file (please note that some columns are simply placeholders, added just to make it work in browser).

And here is the loadTrack snippet I use in the html:

igv.browser.loadTrack({ url: './data/tes-cis-eqtl.txt', name: 'test', format: 'gtexGWAS', featureType: 'gwas', colorScale: { thresholds: [], colors:['rgb(122,179,23)'] },

                                maxLogP: 16,
                                height: 150,
                                label: 'Test'});
        }

Hope this would help.

Thanks!

On Thu, Apr 6, 2017 at 11:38 AM, Jim Robinson notifications@github.com wrote:

OK, that is helpful. Its a bit fortunate this is working at all for you, the flat eqtl files originally supported the gtex portal (thus gtex in the name). However the portal now uses a webservice, as you note, and the eqtl flat files are not supported or tested anymore. I supposed you discovered this format from browsing the source code. Could you provide a small test file, and also a sample web page or track config javascript snippet that uses it?

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SNP_Chr SNP_Pos_hg19 Transcript_GeneSymbol 1:243544827 Rs_ID P-val phen Gene 1 28225114 RPA2 1:243544827 rs1000431 1.45E-18 phen RPA2 4 1324346 CRIPAK 1:243544827 rs10012416 1.43E-14 phen CRIPAK 4 84167984 HPSE 1:243544827 rs10014278 3.19E-05 phen HPSE 4 2862190 MFSD10 1:243544827 rs10026792 7.53E-05 phen MFSD10 4 88292147 HSD17B11 1:243544827 rs10034537 0.000147690179652976 phen HSD17B11 5 176484984 MXD3 1:243544827 rs10035183 0.000101460925956596 phen MXD3 5 95990869 CAST 1:243544827 rs10039522 6.90E-08 phen CAST 12 129625269 SLC15A4 1:243544827 rs10047656 0.00024678557764908 phen SLC15A4 5 176735187 RAB24 1:243544827 rs10051822 0.000109593885762883 phen RAB24 5 35512003 BRIX1 1:243544827 rs10065345 0.000108780888918509 phen BRIX1 5 75803002 PDE8B 1:243544827 rs10066611 0.000136411934082815 phen PDE8B 5 179050918 HNRNPH1 1:243544827 rs10066669 9.47E-08 phen HNRNPH1 5 150123251 C5orf62 1:243544827 rs10068228 6.19E-05 phen C5orf62 5 147547917 FBXO38 1:243544827 rs10068916 2.03E-06 phen FBXO38 5 95990057 CAST 1:243544827 rs10075736 6.04E-13 phen CAST 15 90799802 NGRN 1:243544827 rs10083710 0.000151023197346242 phen NGRN 8 131420688 ASAP1 1:243544827 rs10086773 0.000129773412059186 phen ASAP1 8 28909523 HMBOX1 1:243544827 rs10088428 8.92E-10 phen HMBOX1 8 41234902 GOLGA7 1:243544827 rs10088901 5.14E-05 phen GOLGA7 8 3165777 ??? 1:243544827 rs10091831 0.000122948939352581 phen ??? 5 149492119 DCTN4 1:243544827 rs1009424 0.00023937918604321 phen DCTN4 8 23324877 ENTPD4 1:243544827 rs10094683 1.09E-10 phen ENTPD4 19 48702219 CARD8 1:243544827 rs1010089 7.17E-19 phen CARD8 8 6793006 DEFA4 1:243544827 rs10103091 6.89E-06 phen DEFA4 8 145004944 PLEC1 1:243544827 rs10107388 5.85E-06 phen PLEC1 8 81791762 TPD52 1:243544827 rs10112204 0.000159993599405168 phen TPD52 9 103065265 INVS 1:243544827 rs10124893 2.83E-06 phen INVS 14 21274036 RPGRIP1 1:243544827 rs10131805 6.67E-05 phen RPGRIP1 14 93148543 BTBD7 1:243544827 rs10139162 2.58E-05 phen BTBD7 14 93693604 UBR7 1:243544827 rs10144530 2.83E-05 phen UBR7 14 24899194 KHNYN 1:243544827 rs10146759 5.31E-13 phen KHNYN 14 100838007 SLC25A29 1:243544827 rs10149239 9.30E-14 phen SLC25A29 14 78380965 ADCK1 1:243544827 rs10150472 5.44E-12 phen ADCK1 9 96345328 FAM120AOS 1:243544827 rs10156602 0.000148145375061101 phen FAM120AOS 11 65667149 MUS81 1:243544827 rs10160792 3.08E-06 phen MUS81 18 9542084 PPP4R1 1:243544827 rs10163801 1.66E-05 phen PPP4R1 12 108949966 ISCU 1:243544827 rs1016881 9.13E-14 phen ISCU 2 30449594 LBH 1:243544827 rs10175798 7.77E-08 phen LBH 2 48994107 CCDC128 1:243544827 rs10176937 0.000119569297541119 phen CCDC128 2 85524876 TGOLN2 1:243544827 rs10178604 9.69E-05 phen TGOLN2 2 88949205 RPIA 1:243544827 rs10178815 0.000182640507008978 phen RPIA 2 160427646 BAZ2B 1:243544827 rs10202187 3.79E-13 phen BAZ2B 2 201806597 CASP8 1:243544827 rs10207973 6.55E-05 phen CASP8 2 100075804 REV1 1:243544827 rs10207981 1.27E-05 phen REV1 12 26569724 SSPN 1:243544827 rs1021296 0.000126647925312339 phen SSPN 4 88291760 HSD17B11 1:243544827 rs10213098 0.000260699941189299 phen HSD17B11 4 4864276 LYAR 1:243544827 rs10213148 4.81E-05 phen LYAR 4 175632850 GPM6A 1:243544827 rs10213402 0.000157278996774258 phen GPM6A 7 128599397 IRF5 1:243544827 rs10229001 6.36E-32 phen IRF5 7 128599397 IRF5 1:243544827 rs10229001 7.93E-15 phen IRF5 7 97785669 TECPR1 1:243544827 rs10243469 1.81E-05 phen TECPR1 7 140936088 KIAA1147 1:243544827 rs1024722 0.000197813722609637 phen KIAA1147 7 102022586 LRWD1 1:243544827 rs10249581 6.46E-14 phen LRWD1 7 44584551 ??? 1:243544827 rs10260606 5.52E-05 phen ??? 11 3865786 TRIM68 1:243544827 rs1026231 5.28E-05 phen TRIM68 7 38636891 GPR141 1:243544827 rs10263645 0.00020568202311997 phen GPR141 7 30731993 FAM188B 1:243544827 rs10271601 4.81E-05 phen FAM188B 8 144107977 LY6E 1:243544827 rs10283236 1.05E-08 phen LY6E 9 125157198 PTGS1 1:243544827 rs10306194 6.51E-05 phen PTGS1 4 102223386 FLJ20021 1:243544827 rs1031034 5.81E-13 phen FLJ20021 8 9040858 PPP1R3B 1:243544827 rs1038248 0.000244494555920015 phen PPP1R3B 5 73927752 ENC1 1:243544827 rs1039320 1.66E-32 phen ENC1 5 73927752 HEXB 1:243544827 rs1039320 5.94E-06 phen HEXB 1 203156080 MYBPH 1:243544827 rs10399931 1.68E-17 phen MYBPH 6 111902079 TRAF3IP2 1:243544827 rs1040382 1.48E-08 phen TRAF3IP2 19 40777133 PLD3 1:243544827 rs10405207 0.000143339270974138 phen PLD3 19 45011727 ZNF234 1:243544827 rs10408058 2.87E-05 phen ZNF234 19 20782523 ZNF431 1:243544827 rs10411545 2.02E-05 phen ZNF431 19 43202770 LYPD3 1:243544827 rs10412221 5.34E-05 phen LYPD3 19 2575186 REXO1 1:243544827 rs10419362 0.000118265964613741 phen REXO1 19 42125660 CEACAM4 1:243544827 rs1041994 1.00E-19 phen CEACAM4 19 19383537 KIAA0892 1:243544827 rs10419998 9.62E-16 phen KIAA0892 19 49390878 DHDH 1:243544827 rs10423931 9.19E-05 phen DHDH 5 137902339 PAIP2 1:243544827 rs1042665 3.39E-05 phen PAIP2 6 43753212 ZNF318 1:243544827 rs10434 0.000138460768708134 phen ZNF318 22 42981678 NDUFA6 1:243544827 rs1043606 0.000176163164189338 phen NDUFA6 19 15708779 CYP4F3 1:243544827 rs10439166 0.000157463896249393 phen CYP4F3 2 203055522 CASP8 1:243544827 rs10445793 6.04E-05 phen CASP8 8 17917428 ASAH1 1:243544827 rs10448131 5.10E-11 phen ASAH1 5 132752323 SKP1 1:243544827 rs10452539 0.000283362981110264 phen SKP1 8 142200467 DENND3 1:243544827 rs1045303 2.54E-07 phen DENND3 11 20265876 ??? 1:243544827 rs10458881 0.000246625051048321 phen ??? 19 1095514 GPX4 1:243544827 rs1046040 5.99E-07 phen GPX4 1 22443887 HSPC157 1:243544827 rs1046310 9.80E-11 phen HSPC157 2 74699778 MRPL53 1:243544827 rs1047911 1.98E-05 phen MRPL53 7 73108924 WBSCR22 1:243544827 rs10479665 1.46E-11 phen WBSCR22 1 182542851 RNASEL 1:243544827 rs1048260 3.49E-05 phen RNASEL 6 38979441 C6orf64 1:243544827 rs10484850 7.00E-05 phen C6orf64 10 112053599 SMNDC1 1:243544827 rs1050755 9.51E-07 phen SMNDC1 7 100782460 GNB2 1:243544827 rs1050955 9.57E-05 phen GNB2 5 51955408 PELO 1:243544827 rs10512980 0.000151368076302287 phen PELO 9 111881856 C9orf6 1:243544827 rs1051474 1.18E-05 phen C9orf6 3 127391378 ABTB1 1:243544827 rs1056235 2.03E-07 phen ABTB1 20 7962128 TMX4 1:243544827 rs1058007 4.53E-09 phen TMX4 13 52319678 DHRS12 1:243544827 rs1060562 2.13E-05 phen DHRS12 10 100189138 HPS1 1:243544827 rs1061135 0.000247364364585373 phen HPS1 19 1086211 POLR2E 1:243544827 rs1061233 0.000265642859180972 phen POLR2E 9 135764081 C9orf9 1:243544827 rs1062218 0.000120073510332433 phen C9orf9 7 87835469 SRI 1:243544827 rs1063964 1.59E-05 phen SRI 15 45981317 SQRDL 1:243544827 rs10643 1.63E-08 phen SQRDL 6 32546615 NCR3 1:243544827 rs1064717 8.69E-05 phen NCR3 16 1839134 NME3 1:243544827 rs1065666 5.96E-05 phen NME3 12 1947193 ADIPOR2 1:243544827 rs10735004 2.84E-05 phen ADIPOR2 9 75991893 ANXA1 1:243544827 rs10735622 3.68E-10 phen ANXA1 12 41800488 PPHLN1 1:243544827 rs10735993 0.000262163983886547 phen PPHLN1 14 94353093 MOAP1 1:243544827 rs1073778 6.25E-05 phen MOAP1 9 124021025 GSN 1:243544827 rs10739593 1.04E-07 phen GSN 12 124231355 ATP6V0A2 1:243544827 rs10744161 1.21E-05 phen ATP6V0A2 12 97871380 NEDD1 1:243544827 rs10745798 5.54E-05 phen NEDD1 1 213050209 LQK1 1:243544827 rs10746439 2.50E-16 phen LQK1 12 56077418 BAZ2A 1:243544827 rs10747759 0.000113075797205558 phen BAZ2A 10 101283330 BLOC1S2 1:243544827 rs10748781 8.55E-05 phen BLOC1S2 1 168166616 TIPRL 1:243544827 rs10753766 2.62E-08 phen TIPRL 8 21762915 XPO7 1:243544827 rs1075417 1.88E-05 phen XPO7 9 35776190 GBA2 1:243544827 rs10758322 3.28E-06 phen GBA2 9 104623299 RNF20 1:243544827 rs10760813 5.50E-05 phen RNF20 10 71040106 HNRPH3 1:243544827 rs10762273 0.000163874357199423 phen HNRPH3 11 3914033 STIM1 1:243544827 rs10767685 1.10E-06 phen STIM1 6 36348689 ETV7 1:243544827 rs1076928 6.03E-10 phen ETV7 12 10215582 CLEC9A 1:243544827 rs10772230 9.05E-08 phen CLEC9A 12 10492728 KLRC3 1:243544827 rs10772261 0.000101338522546955 phen KLRC3 12 6242259 VWF 1:243544827 rs10774396 3.75E-14 phen VWF 15 58723426 AQP9 1:243544827 rs1077835 0.000257243207454436 phen AQP9 12 109133588 CORO1C 1:243544827 rs10778656 1.05E-09 phen CORO1C 9 78242109 PCSK5 1:243544827 rs10781300 3.77E-07 phen PCSK5 12 53847473 C12orf10 1:243544827 rs10783580 3.39E-06 phen C12orf10 11 65363865 KAT5 1:243544827 rs10791819 0.000200902878356274 phen KAT5 11 65363865 MAP3K11 1:243544827 rs10791819 3.62E-08 phen MAP3K11 10 7319541 PRKCQ 1:243544827 rs10795539 5.89E-05 phen PRKCQ 1 156735422 C1orf66 1:243544827 rs10796965 0.000149363309105606 phen C1orf66 1 160497984 CD84 1:243544827 rs10797073 1.32E-05 phen CD84 1 182373498 GLUL 1:243544827 rs10797773 6.03E-05 phen GLUL 1 185394834 IVNS1ABP 1:243544827 rs10798014 0.000108398870819528 phen IVNS1ABP 1 33941028 S100PBP 1:243544827 rs10798954 0.000116535220277128 phen S100PBP 1 200508928 CSRP1 1:243544827 rs10800707 0.000278059142334148 phen CSRP1 1 236311886 GPR137B 1:243544827 rs10802285 0.000182938541798671 phen GPR137B 1 236771229 LGALS8 1:243544827 rs10802552 1.30E-07 phen LGALS8 1 15278473 KIAA1026 1:243544827 rs10803327 2.27E-14 phen KIAA1026 7 151633265 GALNT11 1:243544827 rs10807990 2.53E-07 phen GALNT11 7 107552088 BCAP29 1:243544827 rs10808155 7.55E-05 phen BCAP29 1 93854688 DR1 1:243544827 rs1081521 1.81E-10 phen DR1 9 123572038 LOC253039 1:243544827 rs10818476 7.86E-26 phen LOC253039 9 125002275 RBM18 1:243544827 rs10818655 9.36E-05 phen RBM18 10 72064976 TYSND1 1:243544827 rs10823515 9.17E-06 phen TYSND1 10 75464853 SEC24C 1:243544827 rs10824028 4.82E-05 phen SEC24C 11 93370692 C11orf54 1:243544827 rs10831080 0.000202388805446248 phen C11orf54 11 93421782 SNORA25 1:243544827 rs10831093 2.13E-11 phen SNORA25 11 2927670 SLC22A18AS 1:243544827 rs10832888 0.00027600042102939 phen SLC22A18AS 11 7606498 PPFIBP2 1:243544827 rs10839816 2.53E-09 phen PPFIBP2 11 8736695 TRIM66 1:243544827 rs10840114 1.88E-09 phen TRIM66 12 9935825 GABARAPL1 1:243544827 rs10844782 0.000133040249207915 phen GABARAPL1 12 7900184 CLEC4C 1:243544827 rs10845821 2.31E-35 phen CLEC4C 12 131295828 STX2 1:243544827 rs10848208 3.07E-09 phen STX2 12 6412036 PTMS 1:243544827 rs10849438 0.000233577606674428 phen PTMS 12 6654050 HOM-TES-103 1:243544827 rs10849488 3.33E-11 phen HOM-TES-103 15 63100467 RAB8B 1:243544827 rs10851718 7.08E-05 phen RAB8B 1 111733724 CEPT1 1:243544827 rs10857859 8.63E-05 phen CEPT1 9 137857863 FCN1 1:243544827 rs10858304 1.28E-09 phen FCN1 12 92956190 MRPL42 1:243544827 rs10859340 0.000270303041652793 phen MRPL42 12 102293288 DRAM1 1:243544827 rs10860815 5.86E-09 phen DRAM1 1 219260673 LYPLAL1 1:243544827 rs10863423 4.68E-09 phen LYPLAL1 3 49858142 UBA7 1:243544827 rs10865958 8.80E-18 phen UBA7 8 23468924 NKX3-1 1:243544827 rs10866831 1.36E-21 phen NKX3-1 9 140534584 ARRDC1 1:243544827 rs10867035 5.35E-05 phen ARRDC1 9 72313481 PTAR1 1:243544827 rs10867922 1.26E-08 phen PTAR1 9 140006491 MAN1B1 1:243544827 rs10870180 7.00E-09 phen MAN1B1 14 23217371 RBM23 1:243544827 rs10873040 1.57E-05 phen RBM23 12 49012011 C12orf41 1:243544827 rs10875848 1.01E-06 phen C12orf41 12 56050706 DGKA 1:243544827 rs10876844 0.000261124760584804 phen DGKA 3 4114156 TRNT1 1:243544827 rs1087823 5.52E-05 phen TRNT1 12 66872341 HMGA2 1:243544827 rs10878433 0.000158212696704638 phen HMGA2 12 46595290 SLC38A1 1:243544827 rs10880935 0.000226174929538926 phen SLC38A1 10 104973061 C10orf32 1:243544827 rs10883848 6.45E-06 phen C10orf32 1 151068637 CDC42SE1 1:243544827 rs10888404 1.04E-05 phen CDC42SE1 1 153171148 SPRR2D 1:243544827 rs10888535 0.000249047422175854 phen SPRR2D 11 126425577 ST3GAL4 1:243544827 rs10893539 3.55E-05 phen ST3GAL4 11 129698856 TMEM45B 1:243544827 rs10894147 1.76E-18 phen TMEM45B 11 72700779 ATG16L2 1:243544827 rs10898894 0.000204941336870698 phen ATG16L2 11 76600932 PHCA 1:243544827 rs10899303 8.40E-11 phen PHCA 11 960641 RIC8A 1:243544827 rs10902251 1.57E-05 phen RIC8A 1 26666196 AIM1L 1:243544827 rs10902740 2.46E-05 phen AIM1L 10 5541181 RBM17 1:243544827 rs10904516 2.13E-05 phen RBM17 1 154710904 HAX1 1:243544827 rs10908429 7.85E-05 phen HAX1 1 161008535 TSTD1 1:243544827 rs10908821 3.87E-18 phen TSTD1 1 161008535 TSTD1 1:243544827 rs10908821 7.19E-06 phen TSTD1 1 181493767 CACNA1E 1:243544827 rs10910948 8.34E-05 phen CACNA1E 1 183489203 SMG7 1:243544827 rs10911353 7.15E-17 phen SMG7 3 126212567 ZXDC 1:243544827 rs1091553 2.37E-08 phen ZXDC 1 24085063 FUCA1 1:243544827 rs10917423 5.61E-10 phen FUCA1 1 19756869 CAPZB 1:243544827 rs10917449 2.77E-06 phen CAPZB 16 10829280 TXNDC11 1:243544827 rs1091849 0.000186756450729357 phen TXNDC11 2 15737268 DDX1 1:243544827 rs10929377 2.24E-19 phen DDX1 2 10558066 HPCAL1 1:243544827 rs10929663 9.46E-07 phen HPCAL1 6 89569254 RNGTT 1:243544827 rs10944411 2.49E-07 phen RNGTT 7 6541015 AIMP2 1:243544827 rs10951985 0.000137026687318167 phen AIMP2 8 124782340 MTSS1 1:243544827 rs10956148 0.000130050395073069 phen MTSS1 8 38052482 LSM1 1:243544827 rs10958541 2.46E-20 phen LSM1 8 39798341 IDO1 1:243544827 rs10958575 7.76E-06 phen IDO1 9 34151280 NUDT2 1:243544827 rs10971956 1.98E-13 phen NUDT2 9 5433404 JAK2 1:243544827 rs10975114 5.85E-05 phen JAK2 9 100736718 ??? 1:243544827 rs10984599 9.83E-05 phen ??? 9 130611523 C9orf114 1:243544827 rs10987756 0.000171917748382816 phen C9orf114 9 133014623 LOC158301 1:243544827 rs10988658 0.000132175255094301 phen LOC158301 9 95551617 BICD2 1:243544827 rs10992469 1.55E-07 phen BICD2 9 97058302 HIATL1 1:243544827 rs10993151 2.23E-20 phen HIATL1 10 51563993 TIMM23 1:243544827 rs10994675 6.96E-07 phen TIMM23 10 69602892 SIRT1 1:243544827 rs10997828 7.43E-21 phen SIRT1 10 70386834 SUPV3L1 1:243544827 rs10998342 0.000189582196576523 phen SUPV3L1 10 71043781 HNRNPH3 1:243544827 rs10998696 0.00013570880175954 phen HNRNPH3 10 72174390 EIF4EBP2 1:243544827 rs10999323 1.44E-05 phen EIF4EBP2 10 52357891 SGMS1 1:243544827 rs11006259 9.81E-05 phen SGMS1 10 20414564 PLXDC2 1:243544827 rs11011813 0.000192000641223335 phen PLXDC2 10 26706338 YME1L1 1:243544827 rs11015094 0.000269542672528715 phen YME1L1 10 129892160 PTPRE 1:243544827 rs11016068 0.000126519194155101 phen PTPRE 11 29781464 C11orf46 1:243544827 rs11030799 6.74E-05 phen C11orf46 11 32459923 EIF3M 1:243544827 rs11031783 0.000183477239207002 phen EIF3M 11 44723871 CD82 1:243544827 rs11038116 1.44E-05 phen CD82 12 22666996 KIAA0528 1:243544827 rs11046453 0.000102487309033307 phen KIAA0528 12 25051596 BCAT1 1:243544827 rs11047695 5.97E-12 phen BCAT1 4 185304463 IRF2 1:243544827 rs1105207 0.000177850007418945 phen IRF2 1 2141985 C1orf86 1:243544827 rs1105269 2.15E-07 phen C1orf86 12 10283711 CLEC7A 1:243544827 rs11053624 2.10E-06 phen CLEC7A 12 7904111 CLEC4C 1:243544827 rs11055602 5.35E-29 phen CLEC4C 12 123770362 CDK2AP1 1:243544827 rs11057242 1.85E-16 phen CDK2AP1 12 123219785 DENR 1:243544827 rs11059650 1.47E-05 phen DENR 12 6241707 CD9 1:243544827 rs11064041 4.15E-12 phen CD9 12 6705937 NOP2 1:243544827 rs11064275 0.000182335686654493 phen NOP2 13 111172407 RAB20 1:243544827 rs11069851 9.42E-08 phen RAB20 16 25039449 ARHGAP17 1:243544827 rs11074668 9.16E-13 phen ARHGAP17 17 18664378 FLII 1:243544827 rs11078420 1.94E-05 phen FLII 17 3820239 P2RX1 1:243544827 rs11078476 7.12E-24 phen P2RX1 17 40545770 VAT1 1:243544827 rs11079043 9.76E-05 phen VAT1 18 44659001 HDHD2 1:243544827 rs11082563 0.000147466205368872 phen HDHD2 19 3735215 EEF2 1:243544827 rs11085038 0.000173248314549518 phen EEF2 19 9546460 ZNF266 1:243544827 rs11086035 1.17E-11 phen ZNF266 19 9546460 ZNF266 1:243544827 rs11086035 5.88E-21 phen ZNF266 14 20849002 FLJ10357 1:243544827 rs1108614 0.000228205532379093 phen FLJ10357 21 19070092 C21orf91 1:243544827 rs11088649 5.14E-05 phen C21orf91 4 37375277 TBC1D1 1:243544827 rs11096872 6.04E-05 phen TBC1D1 4 100744401 DAPP1 1:243544827 rs11097677 5.13E-05 phen DAPP1 4 159857539 RAPGEF2 1:243544827 rs11100203 1.13E-08 phen RAPGEF2 1 111427656 KCND3 1:243544827 rs11102172 0.000125172667347624 phen KCND3 9 138980277 NACC2 1:243544827 rs11103323 1.56E-07 phen NACC2 12 104192793 NT5DC3 1:243544827 rs11111790 2.21E-05 phen NT5DC3 1 219280033 LYPLAL1 1:243544827 rs11118215 3.93E-08 phen LYPLAL1 1 209938987 TRAF3IP3 1:243544827 rs11119339 9.68E-14 phen TRAF3IP3 1 212955231 NSL1 1:243544827 rs11120025 1.68E-07 phen NSL1 1 10455148 KIF1B 1:243544827 rs11121559 2.29E-07 phen KIF1B 1 231111477 TTC13 1:243544827 rs11122172 4.52E-17 phen TTC13 1 231111477 TTC13 1:243544827 rs11122172 5.20E-15 phen TTC13 2 99884546 MITD1 1:243544827 rs11123777 7.87E-05 phen MITD1 2 3471146 TTC15 1:243544827 rs11127428 9.82E-12 phen TTC15 3 9836312 TADA3 1:243544827 rs11131186 0.000135748205918201 phen TADA3 13 77434603 KCTD12 1:243544827 rs1113312 5.71E-05 phen KCTD12 5 175904141 RNF44 1:243544827 rs11134977 9.98E-06 phen RNF44 9 140380376 FBXW5 1:243544827 rs11137268 4.42E-05 phen FBXW5 6 6810109 F13A1 1:243544827 rs111418267 0.000120255308965732 phen F13A1 9 71184184 PIP5K1B 1:243544827 rs11142965 5.93E-05 phen PIP5K1B 19 876882 CFD 1:243544827 rs111469573 1.24E-08 phen CFD 12 133385721 GOLGA3 1:243544827 rs11147084 4.28E-05 phen GOLGA3 17 259648 C17orf97 1:243544827 rs11150882 1.08E-29 phen C17orf97 17 259648 C17orf97 1:243544827 rs11150882 6.72E-32 phen C17orf97 15 42323272 NUSAP1 1:243544827 rs111532177 0.000245297284230151 phen NUSAP1 6 139099401 CCDC28A 1:243544827 rs11155000 3.79E-05 phen CCDC28A 1 76394910 RABGGTB 1:243544827 rs11161905 3.24E-05 phen RABGGTB 3 134834409 PPP2R3A 1:243544827 rs111621177 1.46E-05 phen PPP2R3A 12 51117593 DIP2B 1:243544827 rs11169530 8.10E-06 phen DIP2B 12 57287522 DCTN2 1:243544827 rs11172038 0.000281833966792196 phen DCTN2 16 1294883 FAM173A 1:243544827 rs111743119 6.02E-05 phen FAM173A 12 62530388 FAM19A2 1:243544827 rs11174342 0.000123227868694894 phen FAM19A2 17 76901058 TIMP2 1:243544827 rs111770145 5.35E-07 phen TIMP2 12 69175793 MDM2 1:243544827 rs11177370 1.10E-05 phen MDM2 12 69175793 SLC35E3 1:243544827 rs11177370 3.30E-09 phen SLC35E3 12 69769275 YEATS4 1:243544827 rs11177631 2.57E-10 phen YEATS4 19 2191796 GNA15 1:243544827 rs111785160 3.45E-05 phen GNA15 12 43405540 YAF2 1:243544827 rs11181845 2.00E-05 phen YAF2 12 47719326 LOC728181 1:243544827 rs11183849 0.000152601059473514 phen LOC728181 20 3052586 SPEF1 1:243544827 rs111869749 7.96E-05 phen SPEF1 8 39816912 INDO 1:243544827 rs111880438 9.26E-05 phen INDO 10 99159096 FRAT1 1:243544827 rs11189203 1.97E-09 phen FRAT1 10 99181008 FRAT2 1:243544827 rs11189214 4.80E-07 phen FRAT2 10 101185830 CHUK 1:243544827 rs11190087 0.000111001703485336 phen CHUK 10 105170649 USMG5 1:243544827 rs11191683 6.63E-43 phen USMG5 10 105245352 C10orf78 1:243544827 rs11191711 0.000190512694944968 phen C10orf78 10 112013274 ??? 1:243544827 rs11195048 0.000129987667599754 phen ??? 10 81931780 ANXA11 1:243544827 rs11201966 9.60E-09 phen ANXA11 10 89895807 ??? 1:243544827 rs11202661 0.000132855090039766 phen ??? 16 88827338 CDK10 1:243544827 rs112028717 7.20E-08 phen CDK10 10 91213935 FAS 1:243544827 rs11203134 6.61E-05 phen FAS 1 151793174 FAM63A 1:243544827 rs11204894 0.000166263169282398 phen FAM63A 1 44474802 CCDC24 1:243544827 rs11210939 1.61E-18 phen CCDC24 1 44541961 MED8 1:243544827 rs11210951 8.22E-06 phen MED8 1 48016189 CMPK1 1:243544827 rs11211551 0.000272660865474489 phen CMPK1 11 108053887 ATM 1:243544827 rs11212542 6.37E-13 phen ATM 11 86683231 ??? 1:243544827 rs112141754 3.61E-06 phen ??? 19 50047311 RCN3 1:243544827 rs112173908 3.44E-08 phen RCN3 20 60243836 OSBPL2 1:243544827 rs1122269 5.43E-05 phen OSBPL2 11 58589305 FAM111A 1:243544827 rs11229642 9.24E-06 phen FAM111A 17 46191032 SP6 1:243544827 rs112306902 8.85E-05 phen SP6 11 64046885 NUDT22 1:243544827 rs11231741 0.000188609303502628 phen NUDT22 10 35550294 CUL2 1:243544827 rs112355105 1.90E-07 phen CUL2 19 46310228 SYMPK 1:243544827 rs112400363 0.000209044895929256 phen SYMPK 2 127419105 GYPC 1:243544827 rs112403595 5.23E-07 phen GYPC 2 127419105 GYPC 1:243544827 rs112403595 5.52E-06 phen GYPC 9 134585181 RAPGEF1 1:243544827 rs11243480 2.68E-12 phen RAPGEF1 10 126323766 FAM53B 1:243544827 rs11245322 0.000239815785106628 phen FAM53B 5 176041931 B4GALT7 1:243544827 rs1124715 0.000220158407224203 phen B4GALT7 2 109042440 GCC2 1:243544827 rs112482682 0.000228421974579343 phen GCC2 10 124814481 ??? 1:243544827 rs11248371 3.21E-05 phen ??? 2 85094533 ST3GAL5 1:243544827 rs112524336 0.000254735041022514 phen ST3GAL5 10 12307894 ??? 1:243544827 rs11257655 1.27E-09 phen ??? 10 12307894 CAMK1D 1:243544827 rs11257655 8.55E-10 phen CAMK1D 10 12307894 CDC123 1:243544827 rs11257655 2.63E-07 phen CDC123 10 14534753 FAM107B 1:243544827 rs11259141 2.73E-06 phen FAM107B 17 34896877 GGNBP2 1:243544827 rs11263770 1.16E-09 phen GGNBP2 1 159976867 PIGM 1:243544827 rs11265305 0.000199657074809162 phen PIGM 16 1853335 HN1L 1:243544827 rs112690906 0.000232718015784108 phen HN1L 1 153779412 GATAD2B 1:243544827 rs1127091 4.61E-06 phen GATAD2B 19 40344366 ITPKC 1:243544827 rs112728066 0.00024888947935896 phen ITPKC 12 124559539 ??? 1:243544827 rs112745336 0.000130133078843364 phen ??? 3 183652932 ABCC5 1:243544827 rs112754234 2.89E-11 phen ABCC5 1 43443376 ELOVL1 1:243544827 rs112761111 0.000253321197068162 phen ELOVL1 11 32648203 PRRG4 1:243544827 rs112773089 1.70E-05 phen PRRG4 7 51091874 GRB10 1:243544827 rs112826922 1.80E-05 phen GRB10 17 40127060 AOC2 1:243544827 rs11296 0.000141658842773418 phen AOC2 7 100892196 CLDN15 1:243544827 rs112971669 8.58E-05 phen CLDN15 7 128755229 LOC286016 1:243544827 rs112984431 0.000157077350629057 phen LOC286016 1 33789968 PHC2 1:243544827 rs1130800 6.04E-06 phen PHC2 17 4637396 ZMYND15 1:243544827 rs1131456 2.42E-07 phen ZMYND15 4 102009720 PPP3CA 1:243544827 rs113159161 7.31E-05 phen PPP3CA 17 17145154 FLCN 1:243544827 rs113161761 4.48E-07 phen FLCN 12 7247395 C1RL 1:243544827 rs1132216 2.22E-07 phen C1RL 19 35919422 ALKBH6 1:243544827 rs113255036 6.96E-06 phen ALKBH6 6 31415150 LOC100129668 1:243544827 rs113286688 8.87E-06 phen LOC100129668 7 1133305 ZFAND2A 1:243544827 rs1133043 6.29E-08 phen ZFAND2A 1 156693135 CRABP2 1:243544827 rs1133856 6.35E-05 phen CRABP2 17 36968710 MED1 1:243544827 rs113435706 0.000245581713543445 phen MED1 16 68335392 NFATC3 1:243544827 rs11350 0.000113774081315591 phen NFATC3 6 15195682 DTNBP1 1:243544827 rs113532504 4.24E-06 phen DTNBP1 8 101765988 RNF19A 1:243544827 rs113657091 1.88E-07 phen RNF19A 3 122036822 CSTA 1:243544827 rs113686831 5.27E-06 phen CSTA 4 39804616 HIP2 1:243544827 rs113769228 6.79E-05 phen HIP2 21 34609596 IFNAR2 1:243544827 rs1137779 4.03E-06 phen IFNAR2 6 32502901 PPT2 1:243544827 rs113787140 0.000271192567216334 phen PPT2 5 142500512 ARHGAP26 1:243544827 rs113801037 9.05E-05 phen ARHGAP26 2 224832136 WDFY1 1:243544827 rs1138616 2.56E-11 phen WDFY1 12 286481 SLC6A13 1:243544827 rs113879277 8.96E-05 phen SLC6A13 6 29832919 HCG9 1:243544827 rs113959448 1.22E-19 phen HCG9 6 31438243 HCP5 1:243544827 rs114034067 0.000203962063658625 phen HCP5 6 30461085 HLA-E 1:243544827 rs114114145 2.05E-07 phen HLA-E 19 33146637 ANKRD27 1:243544827 rs114559145 4.85E-07 phen ANKRD27 6 31667028 EHMT2 1:243544827 rs114627445 2.99E-05 phen EHMT2 5 156987250 ADAM19 1:243544827 rs11465272 3.42E-05 phen ADAM19 5 11032162 ??? 1:243544827 rs114717582 0.000105806056433898 phen ??? 1 174114873 CACYBP 1:243544827 rs1147980 8.07E-05 phen CACYBP 6 31436273 C6orf48 1:243544827 rs114808309 9.83E-05 phen C6orf48 6 33298478 TAPBP 1:243544827 rs114850779 2.32E-07 phen TAPBP 9 93504263 NFIL3 1:243544827 rs1148848 0.000162858098649641 phen NFIL3 1 150930926 ARNT 1:243544827 rs114908993 3.47E-05 phen ARNT 6 13197441 PHACTR1 1:243544827 rs1150598 3.89E-15 phen PHACTR1 7 12261911 TMEM106B 1:243544827 rs11509880 2.20E-10 phen TMEM106B 7 12261911 TMEM106B 1:243544827 rs11509880 3.55E-09 phen TMEM106B 20 62374219 ZGPAT 1:243544827 rs1151626 0.000104982042228872 phen ZGPAT 6 32146657 AIF1 1:243544827 rs115186377 1.08E-07 phen AIF1 9 34162533 UBAP1 1:243544827 rs11521438 6.67E-05 phen UBAP1 14 56945549 NAT12 1:243544827 rs1152547 8.47E-05 phen NAT12 6 30990306 CLIC1 1:243544827 rs115268471 1.18E-05 phen CLIC1 6 29906044 GABBR1 1:243544827 rs115317940 3.85E-06 phen GABBR1 15 45663193 SPATA5L1 1:243544827 rs1153854 2.68E-22 phen SPATA5L1 7 154720259 LOC100132707 1:243544827 rs11543936 3.83E-06 phen LOC100132707 2 85843348 USP39 1:243544827 rs11544042 9.30E-21 phen USP39 12 6602696 VAMP1 1:243544827 rs11545055 5.27E-15 phen VAMP1 19 36246418 U2AF1L4 1:243544827 rs11549030 6.77E-10 phen U2AF1L4 6 31440415 LTA 1:243544827 rs115524885 3.08E-05 phen LTA 17 7462555 TNFSF12 1:243544827 rs11552708 3.29E-09 phen TNFSF12 6 32428397 LOC642073 1:243544827 rs115546460 1.11E-18 phen LOC642073 2 63328774 OTX1 1:243544827 rs115634863 1.50E-09 phen OTX1 7 108011965 CBLL1 1:243544827 rs1156502 0.000129549948192201 phen CBLL1 1 227189642 PSEN2 1:243544827 rs11578103 0.000108361625367859 phen PSEN2 1 161930954 B4GALT3 1:243544827 rs11579627 3.36E-05 phen B4GALT3 9 140413317 C9orf75 1:243544827 rs115803884 0.000261272532836164 phen C9orf75 1 43302515 ERMAP 1:243544827 rs11581978 8.23E-11 phen ERMAP 1 150694777 CTSS 1:243544827 rs11583636 1.02E-09 phen CTSS 1 46656964 UQCRH 1:243544827 rs11584024 2.92E-08 phen UQCRH 1 205034723 NUAK2 1:243544827 rs11588412 7.76E-06 phen NUAK2 1 78575849 USP33 1:243544827 rs11589864 0.000213276803807025 phen USP33 1 207955963 IL20 1:243544827 rs115906510 2.85E-05 phen IL20 10 27821004 RAB18 1:243544827 rs11598492 0.000266826167729231 phen RAB18 11 196944 BET1L 1:243544827 rs11604127 3.66E-06 phen BET1L 11 47725306 MYBPC3 1:243544827 rs11604825 5.44E-09 phen MYBPC3 11 75055107 ARRB1 1:243544827 rs11604864 8.58E-05 phen ARRB1 11 129718478 NFRKB 1:243544827 rs11607337 0.000272910886026419 phen NFRKB 11 62210081 B3GAT3 1:243544827 rs11607566 0.000197821988179421 phen B3GAT3 6 32638146 GPSM3 1:243544827 rs116081545 0.000160755177393362 phen GPSM3 12 29920088 TMTC1 1:243544827 rs11609828 1.74E-14 phen TMTC1 12 125494940 BRI3BP 1:243544827 rs11614174 9.08E-05 phen BRI3BP 12 33019436 C12orf35 1:243544827 rs11615313 2.51E-05 phen C12orf35 9 132613008 FNBP1 1:243544827 rs116214654 6.11E-07 phen FNBP1 14 76470655 C14orf118 1:243544827 rs11623313 0.000164176117100563 phen C14orf118 4 76826582 NAAA 1:243544827 rs116248809 4.86E-16 phen NAAA 14 21347911 RNASE2 1:243544827 rs11626267 4.14E-05 phen RNASE2 14 90968808 CCDC88C 1:243544827 rs11628344 0.000137822895800724 phen CCDC88C 14 24844054 GMPR2 1:243544827 rs11628929 0.000177690090615231 phen GMPR2 15 76608686 ETFA 1:243544827 rs11631423 2.45E-07 phen ETFA 6 31678028 LY6G5C 1:243544827 rs116336999 1.12E-13 phen LY6G5C 6 26208269 ??? 1:243544827 rs116337444 5.43E-27 phen ??? 6 31445771 MICB 1:243544827 rs116345750 2.41E-16 phen MICB 15 75088962 CSK 1:243544827 rs11635664 1.10E-09 phen CSK 15 90882643 IDH2 1:243544827 rs11638227 0.000178232994194828 phen IDH2

[jrobinso]

Sorry no, I'm traveling, will see next week.

2017-04-13 14:38 GMT-04:00 selimkal notifications@github.com:

Hi,

Any progress/feedback on this by any chance?

Thanks!

---------- Forwarded message ---------- From: Selim Kalayci skalayci@gmail.com Date: Mon, Apr 10, 2017 at 4:22 PM Subject: Re: [igvteam/igv] popup window is not opening up in igv.js beta version for gwas track (#385) To: igvteam/igv < reply@reply.github.com

Cc: igvteam/igv igv@noreply.github.com, Author < author@noreply.github.com>

Hi Jim,

I see, good to know about the flat-files/web-service support. And yes, I had seen the usage of flat files for eqtl data in one of the (rather old) test pages I believe.

Attached please find a sample eqtl flat file (please note that some columns are simply placeholders, added just to make it work in browser).

And here is the loadTrack snippet I use in the html:

igv.browser.loadTrack({ url: './data/tes-cis-eqtl.txt', name: 'test', format: 'gtexGWAS',

featureType: 'gwas', colorScale: { thresholds: [], colors:['rgb(122,179,23)'] },

maxLogP: 16, height: 150, label: 'Test'}); }

Hope this would help.

Thanks!

On Thu, Apr 6, 2017 at 11:38 AM, Jim Robinson notifications@github.com wrote:

OK, that is helpful. Its a bit fortunate this is working at all for you, the flat eqtl files originally supported the gtex portal (thus gtex in the name). However the portal now uses a webservice, as you note, and the eqtl flat files are not supported or tested anymore. I supposed you discovered this format from browsing the source code. Could you provide a small test file, and also a sample web page or track config javascript snippet that uses it?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/385#issuecomment-292213935, or mute the thread https://github.com/notifications/unsubscribe-auth/ANWk78_4Vj9O43p_ gshlwDR2ZS6jtBiXks5rtQcIgaJpZM4MzFNa .

SNP_Chr SNP_Pos_hg19 Transcript_GeneSymbol 1:243544827 Rs_ID P-val phen Gene 1 28225114 RPA2 1:243544827 rs1000431 1.45E-18 phen RPA2 4 1324346 CRIPAK 1:243544827 rs10012416 1.43E-14 phen CRIPAK 4 84167984 HPSE 1:243544827 rs10014278 3.19E-05 phen HPSE 4 2862190 MFSD10 1:243544827 rs10026792 7.53E-05 phen MFSD10 4 88292147 HSD17B11 1:243544827 rs10034537 0.000147690179652976 phen HSD17B11 5 176484984 MXD3 1:243544827 rs10035183 0.000101460925956596 phen MXD3 5 95990869 CAST 1:243544827 rs10039522 6.90E-08 phen CAST 12 129625269 SLC15A4 1:243544827 rs10047656 0.00024678557764908 phen SLC15A4 5 176735187 RAB24 1:243544827 rs10051822 0.000109593885762883 phen RAB24 5 35512003 BRIX1 1:243544827 rs10065345 0.000108780888918509 phen BRIX1 5 75803002 PDE8B 1:243544827 rs10066611 0.000136411934082815 phen PDE8B 5 179050918 HNRNPH1 1:243544827 rs10066669 9.47E-08 phen HNRNPH1 5 150123251 C5orf62 1:243544827 rs10068228 6.19E-05 phen C5orf62 5 147547917 FBXO38 1:243544827 rs10068916 2.03E-06 phen FBXO38 5 95990057 CAST 1:243544827 rs10075736 6.04E-13 phen CAST 15 90799802 NGRN 1:243544827 rs10083710 0.000151023197346242 phen NGRN 8 131420688 ASAP1 1:243544827 rs10086773 0.000129773412059186 phen ASAP1 8 28909523 HMBOX1 1:243544827 rs10088428 8.92E-10 phen HMBOX1 8 41234902 GOLGA7 1:243544827 rs10088901 5.14E-05 phen GOLGA7 8 3165777 ??? 1:243544827 rs10091831 0.000122948939352581 phen ??? 5 149492119 DCTN4 1:243544827 rs1009424 0.00023937918604321 phen DCTN4 8 23324877 ENTPD4 1:243544827 rs10094683 1.09E-10 phen ENTPD4 19 48702219 CARD8 1:243544827 rs1010089 7.17E-19 phen CARD8 8 6793006 DEFA4 1:243544827 rs10103091 6.89E-06 phen DEFA4 8 145004944 PLEC1 1:243544827 rs10107388 5.85E-06 phen PLEC1 8 81791762 TPD52 1:243544827 rs10112204 0.000159993599405168 phen TPD52 9 103065265 INVS 1:243544827 rs10124893 2.83E-06 phen INVS 14 21274036 RPGRIP1 1:243544827 rs10131805 6.67E-05 phen RPGRIP1 14 93148543 BTBD7 1:243544827 rs10139162 2.58E-05 phen BTBD7 14 93693604 UBR7 1:243544827 rs10144530 2.83E-05 phen UBR7 14 24899194 KHNYN 1:243544827 rs10146759 5.31E-13 phen KHNYN 14 100838007 SLC25A29 1:243544827 rs10149239 9.30E-14 phen SLC25A29 14 78380965 ADCK1 1:243544827 rs10150472 5.44E-12 phen ADCK1 9 96345328 FAM120AOS 1:243544827 rs10156602 0.000148145375061101 phen FAM120AOS 11 65667149 MUS81 1:243544827 rs10160792 3.08E-06 phen MUS81 18 9542084 PPP4R1 1:243544827 rs10163801 1.66E-05 phen PPP4R1 12 108949966 ISCU 1:243544827 rs1016881 9.13E-14 phen ISCU 2 30449594 LBH 1:243544827 rs10175798 7.77E-08 phen LBH 2 48994107 CCDC128 1:243544827 rs10176937 0.000119569297541119 phen CCDC128 2 85524876 TGOLN2 1:243544827 rs10178604 9.69E-05 phen TGOLN2 2 88949205 RPIA 1:243544827 rs10178815 0.000182640507008978 phen RPIA 2 160427646 BAZ2B 1:243544827 rs10202187 3.79E-13 phen BAZ2B 2 201806597 CASP8 1:243544827 rs10207973 6.55E-05 phen CASP8 2 100075804 REV1 1:243544827 rs10207981 1.27E-05 phen REV1 12 26569724 SSPN 1:243544827 rs1021296 0.000126647925312339 phen SSPN 4 88291760 HSD17B11 1:243544827 rs10213098 0.000260699941189299 phen HSD17B11 4 4864276 LYAR 1:243544827 rs10213148 4.81E-05 phen LYAR 4 175632850 GPM6A 1:243544827 rs10213402 0.000157278996774258 phen GPM6A 7 128599397 IRF5 1:243544827 rs10229001 6.36E-32 phen IRF5 7 128599397 IRF5 1:243544827 rs10229001 7.93E-15 phen IRF5 7 97785669 TECPR1 1:243544827 rs10243469 1.81E-05 phen TECPR1 7 140936088 KIAA1147 1:243544827 rs1024722 0.000197813722609637 phen KIAA1147 7 102022586 LRWD1 1:243544827 rs10249581 6.46E-14 phen LRWD1 7 44584551 ??? 1:243544827 rs10260606 5.52E-05 phen ??? 11 3865786 TRIM68 1:243544827 rs1026231 5.28E-05 phen TRIM68 7 38636891 GPR141 1:243544827 rs10263645 0.00020568202311997 phen GPR141 7 30731993 FAM188B 1:243544827 rs10271601 4.81E-05 phen FAM188B 8 144107977 LY6E 1:243544827 rs10283236 1.05E-08 phen LY6E 9 125157198 PTGS1 1:243544827 rs10306194 6.51E-05 phen PTGS1 4 102223386 FLJ20021 1:243544827 rs1031034 5.81E-13 phen FLJ20021 8 9040858 PPP1R3B 1:243544827 rs1038248 0.000244494555920015 phen PPP1R3B 5 73927752 ENC1 1:243544827 rs1039320 1.66E-32 phen ENC1 5 73927752 HEXB 1:243544827 rs1039320 5.94E-06 phen HEXB 1 203156080 MYBPH 1:243544827 rs10399931 1.68E-17 phen MYBPH 6 111902079 TRAF3IP2 1:243544827 rs1040382 1.48E-08 phen TRAF3IP2 19 40777133 PLD3 1:243544827 rs10405207 0.000143339270974138 phen PLD3 19 45011727 ZNF234 1:243544827 rs10408058 2.87E-05 phen ZNF234 19 20782523 ZNF431 1:243544827 rs10411545 2.02E-05 phen ZNF431 19 43202770 LYPD3 1:243544827 rs10412221 5.34E-05 phen LYPD3 19 2575186 REXO1 1:243544827 rs10419362 0.000118265964613741 phen REXO1 19 42125660 CEACAM4 1:243544827 rs1041994 1.00E-19 phen CEACAM4 19 19383537 KIAA0892 1:243544827 rs10419998 9.62E-16 phen KIAA0892 19 49390878 DHDH 1:243544827 rs10423931 9.19E-05 phen DHDH 5 137902339 PAIP2 1:243544827 rs1042665 3.39E-05 phen PAIP2 6 43753212 ZNF318 1:243544827 rs10434 0.000138460768708134 phen ZNF318 22 42981678 NDUFA6 1:243544827 rs1043606 0.000176163164189338 phen NDUFA6 19 15708779 CYP4F3 1:243544827 rs10439166 0.000157463896249393 phen CYP4F3 2 203055522 CASP8 1:243544827 rs10445793 6.04E-05 phen CASP8 8 17917428 ASAH1 1:243544827 rs10448131 5.10E-11 phen ASAH1 5 132752323 SKP1 1:243544827 rs10452539 0.000283362981110264 phen SKP1 8 142200467 DENND3 1:243544827 rs1045303 2.54E-07 phen DENND3 11 20265876 ??? 1:243544827 rs10458881 0.000246625051048321 phen ??? 19 1095514 GPX4 1:243544827 rs1046040 5.99E-07 phen GPX4 1 22443887 HSPC157 1:243544827 rs1046310 9.80E-11 phen HSPC157 2 74699778 MRPL53 1:243544827 rs1047911 1.98E-05 phen MRPL53 7 73108924 WBSCR22 1:243544827 rs10479665 1.46E-11 phen WBSCR22 1 182542851 RNASEL 1:243544827 rs1048260 3.49E-05 phen RNASEL 6 38979441 C6orf64 1:243544827 rs10484850 7.00E-05 phen C6orf64 10 112053599 SMNDC1 1:243544827 rs1050755 9.51E-07 phen SMNDC1 7 100782460 GNB2 1:243544827 rs1050955 9.57E-05 phen GNB2 5 51955408 PELO 1:243544827 rs10512980 0.000151368076302287 phen PELO 9 111881856 C9orf6 1:243544827 rs1051474 1.18E-05 phen C9orf6 3 127391378 ABTB1 1:243544827 rs1056235 2.03E-07 phen ABTB1 20 7962128 TMX4 1:243544827 rs1058007 4.53E-09 phen TMX4 13 52319678 DHRS12 1:243544827 rs1060562 2.13E-05 phen DHRS12 10 100189138 HPS1 1:243544827 rs1061135 0.000247364364585373 phen HPS1 19 1086211 POLR2E 1:243544827 rs1061233 0.000265642859180972 phen POLR2E 9 135764081 C9orf9 1:243544827 rs1062218 0.000120073510332433 phen C9orf9 7 87835469 SRI 1:243544827 rs1063964 1.59E-05 phen SRI 15 45981317 SQRDL 1:243544827 rs10643 1.63E-08 phen SQRDL 6 32546615 NCR3 1:243544827 rs1064717 8.69E-05 phen NCR3 16 1839134 NME3 1:243544827 rs1065666 5.96E-05 phen NME3 12 1947193 ADIPOR2 1:243544827 rs10735004 2.84E-05 phen ADIPOR2 9 75991893 ANXA1 1:243544827 rs10735622 3.68E-10 phen ANXA1 12 41800488 PPHLN1 1:243544827 rs10735993 0.000262163983886547 phen PPHLN1 14 94353093 MOAP1 1:243544827 rs1073778 6.25E-05 phen MOAP1 9 124021025 GSN 1:243544827 rs10739593 1.04E-07 phen GSN 12 124231355 ATP6V0A2 1:243544827 rs10744161 1.21E-05 phen ATP6V0A2 12 97871380 NEDD1 1:243544827 rs10745798 5.54E-05 phen NEDD1 1 213050209 LQK1 1:243544827 rs10746439 2.50E-16 phen LQK1 12 56077418 BAZ2A 1:243544827 rs10747759 0.000113075797205558 phen BAZ2A 10 101283330 BLOC1S2 1:243544827 rs10748781 8.55E-05 phen BLOC1S2 1 168166616 TIPRL 1:243544827 rs10753766 2.62E-08 phen TIPRL 8 21762915 XPO7 1:243544827 rs1075417 1.88E-05 phen XPO7 9 35776190 GBA2 1:243544827 rs10758322 3.28E-06 phen GBA2 9 104623299 RNF20 1:243544827 rs10760813 5.50E-05 phen RNF20 10 71040106 HNRPH3 1:243544827 rs10762273 0.000163874357199423 phen HNRPH3 11 3914033 STIM1 1:243544827 rs10767685 1.10E-06 phen STIM1 6 36348689 ETV7 1:243544827 rs1076928 6.03E-10 phen ETV7 12 10215582 CLEC9A 1:243544827 rs10772230 9.05E-08 phen CLEC9A 12 10492728 KLRC3 1:243544827 rs10772261 0.000101338522546955 phen KLRC3 12 6242259 VWF 1:243544827 rs10774396 3.75E-14 phen VWF 15 58723426 AQP9 1:243544827 rs1077835 0.000257243207454436 phen AQP9 12 109133588 CORO1C 1:243544827 rs10778656 1.05E-09 phen CORO1C 9 78242109 PCSK5 1:243544827 rs10781300 3.77E-07 phen PCSK5 12 53847473 C12orf10 1:243544827 rs10783580 3.39E-06 phen C12orf10 11 65363865 KAT5 1:243544827 rs10791819 0.000200902878356274 phen KAT5 11 65363865 MAP3K11 1:243544827 rs10791819 3.62E-08 phen MAP3K11 10 7319541 PRKCQ 1:243544827 rs10795539 5.89E-05 phen PRKCQ 1 156735422 C1orf66 1:243544827 rs10796965 0.000149363309105606 phen C1orf66 1 160497984 CD84 1:243544827 rs10797073 1.32E-05 phen CD84 1 182373498 GLUL 1:243544827 rs10797773 6.03E-05 phen GLUL 1 185394834 IVNS1ABP 1:243544827 rs10798014 0.000108398870819528 phen IVNS1ABP 1 33941028 S100PBP 1:243544827 rs10798954 0.000116535220277128 phen S100PBP 1 200508928 CSRP1 1:243544827 rs10800707 0.000278059142334148 phen CSRP1 1 236311886 GPR137B 1:243544827 rs10802285 0.000182938541798671 phen GPR137B 1 236771229 LGALS8 1:243544827 rs10802552 1.30E-07 phen LGALS8 1 15278473 KIAA1026 1:243544827 rs10803327 2.27E-14 phen KIAA1026 7 151633265 GALNT11 1:243544827 rs10807990 2.53E-07 phen GALNT11 7 107552088 BCAP29 1:243544827 rs10808155 7.55E-05 phen BCAP29 1 93854688 DR1 1:243544827 rs1081521 1.81E-10 phen DR1 9 123572038 LOC253039 1:243544827 rs10818476 7.86E-26 phen LOC253039 9 125002275 RBM18 1:243544827 rs10818655 9.36E-05 phen RBM18 10 72064976 TYSND1 1:243544827 rs10823515 9.17E-06 phen TYSND1 10 75464853 SEC24C 1:243544827 rs10824028 4.82E-05 phen SEC24C 11 93370692 C11orf54 1:243544827 rs10831080 0.000202388805446248 phen C11orf54 11 93421782 SNORA25 1:243544827 rs10831093 2.13E-11 phen SNORA25 11 2927670 SLC22A18AS 1:243544827 rs10832888 0.00027600042102939 phen SLC22A18AS 11 7606498 PPFIBP2 1:243544827 rs10839816 2.53E-09 phen PPFIBP2 11 8736695 TRIM66 1:243544827 rs10840114 1.88E-09 phen TRIM66 12 9935825 GABARAPL1 1:243544827 rs10844782 0.000133040249207915 phen GABARAPL1 12 7900184 CLEC4C 1:243544827 rs10845821 2.31E-35 phen CLEC4C 12 131295828 STX2 1:243544827 rs10848208 3.07E-09 phen STX2 12 6412036 PTMS 1:243544827 rs10849438 0.000233577606674428 phen PTMS 12 6654050 HOM-TES-103 1:243544827 rs10849488 3.33E-11 phen HOM-TES-103 15 63100467 RAB8B 1:243544827 rs10851718 7.08E-05 phen RAB8B 1 111733724 CEPT1 1:243544827 rs10857859 8.63E-05 phen CEPT1 9 137857863 FCN1 1:243544827 rs10858304 1.28E-09 phen FCN1 12 92956190 MRPL42 1:243544827 rs10859340 0.000270303041652793 phen MRPL42 12 102293288 DRAM1 1:243544827 rs10860815 5.86E-09 phen DRAM1 1 219260673 LYPLAL1 1:243544827 rs10863423 4.68E-09 phen LYPLAL1 3 49858142 UBA7 1:243544827 rs10865958 8.80E-18 phen UBA7 8 23468924 NKX3-1 1:243544827 rs10866831 1.36E-21 phen NKX3-1 9 140534584 ARRDC1 1:243544827 rs10867035 5.35E-05 phen ARRDC1 9 72313481 PTAR1 1:243544827 rs10867922 1.26E-08 phen PTAR1 9 140006491 MAN1B1 1:243544827 rs10870180 7.00E-09 phen MAN1B1 14 23217371 RBM23 1:243544827 rs10873040 1.57E-05 phen RBM23 12 49012011 C12orf41 1:243544827 rs10875848 1.01E-06 phen C12orf41 12 56050706 DGKA 1:243544827 rs10876844 0.000261124760584804 phen DGKA 3 4114156 TRNT1 1:243544827 rs1087823 5.52E-05 phen TRNT1 12 66872341 HMGA2 1:243544827 rs10878433 0.000158212696704638 phen HMGA2 12 46595290 SLC38A1 1:243544827 rs10880935 0.000226174929538926 phen SLC38A1 10 104973061 C10orf32 1:243544827 rs10883848 6.45E-06 phen C10orf32 1 151068637 CDC42SE1 1:243544827 rs10888404 1.04E-05 phen CDC42SE1 1 153171148 SPRR2D 1:243544827 rs10888535 0.000249047422175854 phen SPRR2D 11 126425577 ST3GAL4 1:243544827 rs10893539 3.55E-05 phen ST3GAL4 11 129698856 TMEM45B 1:243544827 rs10894147 1.76E-18 phen TMEM45B 11 72700779 ATG16L2 1:243544827 rs10898894 0.000204941336870698 phen ATG16L2 11 76600932 PHCA 1:243544827 rs10899303 8.40E-11 phen PHCA 11 960641 RIC8A 1:243544827 rs10902251 1.57E-05 phen RIC8A 1 26666196 AIM1L 1:243544827 rs10902740 2.46E-05 phen AIM1L 10 5541181 RBM17 1:243544827 rs10904516 2.13E-05 phen RBM17 1 154710904 HAX1 1:243544827 rs10908429 7.85E-05 phen HAX1 1 161008535 TSTD1 1:243544827 rs10908821 3.87E-18 phen TSTD1 1 161008535 TSTD1 1:243544827 rs10908821 7.19E-06 phen TSTD1 1 181493767 CACNA1E 1:243544827 rs10910948 8.34E-05 phen CACNA1E 1 183489203 SMG7 1:243544827 rs10911353 7.15E-17 phen SMG7 3 126212567 ZXDC 1:243544827 rs1091553 2.37E-08 phen ZXDC 1 24085063 FUCA1 1:243544827 rs10917423 5.61E-10 phen FUCA1 1 19756869 CAPZB 1:243544827 rs10917449 2.77E-06 phen CAPZB 16 10829280 TXNDC11 1:243544827 rs1091849 0.000186756450729357 phen TXNDC11 2 15737268 DDX1 1:243544827 rs10929377 2.24E-19 phen DDX1 2 10558066 HPCAL1 1:243544827 rs10929663 9.46E-07 phen HPCAL1 6 89569254 RNGTT 1:243544827 rs10944411 2.49E-07 phen RNGTT 7 6541015 AIMP2 1:243544827 rs10951985 0.000137026687318167 phen AIMP2 8 124782340 MTSS1 1:243544827 rs10956148 0.000130050395073069 phen MTSS1 8 38052482 LSM1 1:243544827 rs10958541 2.46E-20 phen LSM1 8 39798341 IDO1 1:243544827 rs10958575 7.76E-06 phen IDO1 9 34151280 NUDT2 1:243544827 rs10971956 1.98E-13 phen NUDT2 9 5433404 JAK2 1:243544827 rs10975114 5.85E-05 phen JAK2 9 100736718 ??? 1:243544827 rs10984599 9.83E-05 phen ??? 9 130611523 C9orf114 1:243544827 rs10987756 0.000171917748382816 phen C9orf114 9 133014623 LOC158301 1:243544827 rs10988658 0.000132175255094301 phen LOC158301 9 95551617 BICD2 1:243544827 rs10992469 1.55E-07 phen BICD2 9 97058302 HIATL1 1:243544827 rs10993151 2.23E-20 phen HIATL1 10 51563993 TIMM23 1:243544827 rs10994675 6.96E-07 phen TIMM23 10 69602892 SIRT1 1:243544827 rs10997828 7.43E-21 phen SIRT1 10 70386834 SUPV3L1 1:243544827 rs10998342 0.000189582196576523 phen SUPV3L1 10 71043781 HNRNPH3 1:243544827 rs10998696 0.00013570880175954 phen HNRNPH3 10 72174390 EIF4EBP2 1:243544827 rs10999323 1.44E-05 phen EIF4EBP2 10 52357891 SGMS1 1:243544827 rs11006259 9.81E-05 phen SGMS1 10 20414564 PLXDC2 1:243544827 rs11011813 0.000192000641223335 phen PLXDC2 10 26706338 YME1L1 1:243544827 rs11015094 0.000269542672528715 phen YME1L1 10 129892160 PTPRE 1:243544827 rs11016068 0.000126519194155101 phen PTPRE 11 29781464 C11orf46 1:243544827 rs11030799 6.74E-05 phen C11orf46 11 32459923 EIF3M 1:243544827 rs11031783 0.000183477239207002 phen EIF3M 11 44723871 CD82 1:243544827 rs11038116 1.44E-05 phen CD82 12 22666996 KIAA0528 1:243544827 rs11046453 0.000102487309033307 phen KIAA0528 12 25051596 BCAT1 1:243544827 rs11047695 5.97E-12 phen BCAT1 4 185304463 IRF2 1:243544827 rs1105207 0.000177850007418945 phen IRF2 1 2141985 C1orf86 1:243544827 rs1105269 2.15E-07 phen C1orf86 12 10283711 CLEC7A 1:243544827 rs11053624 2.10E-06 phen CLEC7A 12 7904111 CLEC4C 1:243544827 rs11055602 5.35E-29 phen CLEC4C 12 123770362 CDK2AP1 1:243544827 rs11057242 1.85E-16 phen CDK2AP1 12 123219785 DENR 1:243544827 rs11059650 1.47E-05 phen DENR 12 6241707 CD9 1:243544827 rs11064041 4.15E-12 phen CD9 12 6705937 NOP2 1:243544827 rs11064275 0.000182335686654493 phen NOP2 13 111172407 RAB20 1:243544827 rs11069851 9.42E-08 phen RAB20 16 25039449 ARHGAP17 1:243544827 rs11074668 9.16E-13 phen ARHGAP17 17 18664378 FLII 1:243544827 rs11078420 1.94E-05 phen FLII 17 3820239 P2RX1 1:243544827 rs11078476 7.12E-24 phen P2RX1 17 40545770 VAT1 1:243544827 rs11079043 9.76E-05 phen VAT1 18 44659001 HDHD2 1:243544827 rs11082563 0.000147466205368872 phen HDHD2 19 3735215 EEF2 1:243544827 rs11085038 0.000173248314549518 phen EEF2 19 9546460 ZNF266 1:243544827 rs11086035 1.17E-11 phen ZNF266 19 9546460 ZNF266 1:243544827 rs11086035 5.88E-21 phen ZNF266 14 20849002 FLJ10357 1:243544827 rs1108614 0.000228205532379093 phen FLJ10357 21 19070092 C21orf91 1:243544827 rs11088649 5.14E-05 phen C21orf91 4 37375277 TBC1D1 1:243544827 rs11096872 6.04E-05 phen TBC1D1 4 100744401 DAPP1 1:243544827 rs11097677 5.13E-05 phen DAPP1 4 159857539 RAPGEF2 1:243544827 rs11100203 1.13E-08 phen RAPGEF2 1 111427656 KCND3 1:243544827 rs11102172 0.000125172667347624 phen KCND3 9 138980277 NACC2 1:243544827 rs11103323 1.56E-07 phen NACC2 12 104192793 NT5DC3 1:243544827 rs11111790 2.21E-05 phen NT5DC3 1 219280033 LYPLAL1 1:243544827 rs11118215 3.93E-08 phen LYPLAL1 1 209938987 TRAF3IP3 1:243544827 rs11119339 9.68E-14 phen TRAF3IP3 1 212955231 NSL1 1:243544827 rs11120025 1.68E-07 phen NSL1 1 10455148 KIF1B 1:243544827 rs11121559 2.29E-07 phen KIF1B 1 231111477 TTC13 1:243544827 rs11122172 4.52E-17 phen TTC13 1 231111477 TTC13 1:243544827 rs11122172 5.20E-15 phen TTC13 2 99884546 MITD1 1:243544827 rs11123777 7.87E-05 phen MITD1 2 3471146 TTC15 1:243544827 rs11127428 9.82E-12 phen TTC15 3 9836312 TADA3 1:243544827 rs11131186 0.000135748205918201 phen TADA3 13 77434603 KCTD12 1:243544827 rs1113312 5.71E-05 phen KCTD12 5 175904141 RNF44 1:243544827 rs11134977 9.98E-06 phen RNF44 9 140380376 FBXW5 1:243544827 rs11137268 4.42E-05 phen FBXW5 6 6810109 F13A1 1:243544827 rs111418267 0.000120255308965732 phen F13A1 9 71184184 PIP5K1B 1:243544827 rs11142965 5.93E-05 phen PIP5K1B 19 876882 CFD 1:243544827 rs111469573 1.24E-08 phen CFD 12 133385721 GOLGA3 1:243544827 rs11147084 4.28E-05 phen GOLGA3 17 259648 C17orf97 1:243544827 rs11150882 1.08E-29 phen C17orf97 17 259648 C17orf97 1:243544827 rs11150882 6.72E-32 phen C17orf97 15 42323272 NUSAP1 1:243544827 rs111532177 0.000245297284230151 phen NUSAP1 6 139099401 CCDC28A 1:243544827 rs11155000 3.79E-05 phen CCDC28A 1 76394910 RABGGTB 1:243544827 rs11161905 3.24E-05 phen RABGGTB 3 134834409 PPP2R3A 1:243544827 rs111621177 1.46E-05 phen PPP2R3A 12 51117593 DIP2B 1:243544827 rs11169530 8.10E-06 phen DIP2B 12 57287522 DCTN2 1:243544827 rs11172038 0.000281833966792196 phen DCTN2 16 1294883 FAM173A 1:243544827 rs111743119 6.02E-05 phen FAM173A 12 62530388 FAM19A2 1:243544827 rs11174342 0.000123227868694894 phen FAM19A2 17 76901058 TIMP2 1:243544827 rs111770145 5.35E-07 phen TIMP2 12 69175793 MDM2 1:243544827 rs11177370 1.10E-05 phen MDM2 12 69175793 SLC35E3 1:243544827 rs11177370 3.30E-09 phen SLC35E3 12 69769275 YEATS4 1:243544827 rs11177631 2.57E-10 phen YEATS4 19 2191796 GNA15 1:243544827 rs111785160 3.45E-05 phen GNA15 12 43405540 YAF2 1:243544827 rs11181845 2.00E-05 phen YAF2 12 47719326 LOC728181 1:243544827 rs11183849 0.000152601059473514 phen LOC728181 20 3052586 SPEF1 1:243544827 rs111869749 7.96E-05 phen SPEF1 8 39816912 INDO 1:243544827 rs111880438 9.26E-05 phen INDO 10 99159096 FRAT1 1:243544827 rs11189203 1.97E-09 phen FRAT1 10 99181008 FRAT2 1:243544827 rs11189214 4.80E-07 phen FRAT2 10 101185830 CHUK 1:243544827 rs11190087 0.000111001703485336 phen CHUK 10 105170649 USMG5 1:243544827 rs11191683 6.63E-43 phen USMG5 10 105245352 C10orf78 1:243544827 rs11191711 0.000190512694944968 phen C10orf78 10 112013274 ??? 1:243544827 rs11195048 0.000129987667599754 phen ??? 10 81931780 ANXA11 1:243544827 rs11201966 9.60E-09 phen ANXA11 10 89895807 ??? 1:243544827 rs11202661 0.000132855090039766 phen ??? 16 88827338 CDK10 1:243544827 rs112028717 7.20E-08 phen CDK10 10 91213935 FAS 1:243544827 rs11203134 6.61E-05 phen FAS 1 151793174 FAM63A 1:243544827 rs11204894 0.000166263169282398 phen FAM63A 1 44474802 CCDC24 1:243544827 rs11210939 1.61E-18 phen CCDC24 1 44541961 MED8 1:243544827 rs11210951 8.22E-06 phen MED8 1 48016189 CMPK1 1:243544827 rs11211551 0.000272660865474489 phen CMPK1 11 108053887 ATM 1:243544827 rs11212542 6.37E-13 phen ATM 11 86683231 ??? 1:243544827 rs112141754 3.61E-06 phen ??? 19 50047311 RCN3 1:243544827 rs112173908 3.44E-08 phen RCN3 20 60243836 OSBPL2 1:243544827 rs1122269 5.43E-05 phen OSBPL2 11 58589305 FAM111A 1:243544827 rs11229642 9.24E-06 phen FAM111A 17 46191032 SP6 1:243544827 rs112306902 8.85E-05 phen SP6 11 64046885 NUDT22 1:243544827 rs11231741 0.000188609303502628 phen NUDT22 10 35550294 CUL2 1:243544827 rs112355105 1.90E-07 phen CUL2 19 46310228 SYMPK 1:243544827 rs112400363 0.000209044895929256 phen SYMPK 2 127419105 GYPC 1:243544827 rs112403595 5.23E-07 phen GYPC 2 127419105 GYPC 1:243544827 rs112403595 5.52E-06 phen GYPC 9 134585181 RAPGEF1 1:243544827 rs11243480 2.68E-12 phen RAPGEF1 10 126323766 FAM53B 1:243544827 rs11245322 0.000239815785106628 phen FAM53B 5 176041931 B4GALT7 1:243544827 rs1124715 0.000220158407224203 phen B4GALT7 2 109042440 GCC2 1:243544827 rs112482682 0.000228421974579343 phen GCC2 10 124814481 ??? 1:243544827 rs11248371 3.21E-05 phen ??? 2 85094533 ST3GAL5 1:243544827 rs112524336 0.000254735041022514 phen ST3GAL5 10 12307894 ??? 1:243544827 rs11257655 1.27E-09 phen ??? 10 12307894 CAMK1D 1:243544827 rs11257655 8.55E-10 phen CAMK1D 10 12307894 CDC123 1:243544827 rs11257655 2.63E-07 phen CDC123 10 14534753 FAM107B 1:243544827 rs11259141 2.73E-06 phen FAM107B 17 34896877 GGNBP2 1:243544827 rs11263770 1.16E-09 phen GGNBP2 1 159976867 PIGM 1:243544827 rs11265305 0.000199657074809162 phen PIGM 16 1853335 HN1L 1:243544827 rs112690906 0.000232718015784108 phen HN1L 1 153779412 GATAD2B 1:243544827 rs1127091 4.61E-06 phen GATAD2B 19 40344366 ITPKC 1:243544827 rs112728066 0.00024888947935896 phen ITPKC 12 124559539 ??? 1:243544827 rs112745336 0.000130133078843364 phen ??? 3 183652932 ABCC5 1:243544827 rs112754234 2.89E-11 phen ABCC5 1 43443376 ELOVL1 1:243544827 rs112761111 0.000253321197068162 phen ELOVL1 11 32648203 PRRG4 1:243544827 rs112773089 1.70E-05 phen PRRG4 7 51091874 GRB10 1:243544827 rs112826922 1.80E-05 phen GRB10 17 40127060 AOC2 1:243544827 rs11296 0.000141658842773418 phen AOC2 7 100892196 CLDN15 1:243544827 rs112971669 8.58E-05 phen CLDN15 7 128755229 LOC286016 1:243544827 rs112984431 0.000157077350629057 phen LOC286016 1 33789968 PHC2 1:243544827 rs1130800 6.04E-06 phen PHC2 17 4637396 ZMYND15 1:243544827 rs1131456 2.42E-07 phen ZMYND15 4 102009720 PPP3CA 1:243544827 rs113159161 7.31E-05 phen PPP3CA 17 17145154 FLCN 1:243544827 rs113161761 4.48E-07 phen FLCN 12 7247395 C1RL 1:243544827 rs1132216 2.22E-07 phen C1RL 19 35919422 ALKBH6 1:243544827 rs113255036 6.96E-06 phen ALKBH6 6 31415150 LOC100129668 1:243544827 rs113286688 8.87E-06 phen LOC100129668 7 1133305 ZFAND2A 1:243544827 rs1133043 6.29E-08 phen ZFAND2A 1 156693135 CRABP2 1:243544827 rs1133856 6.35E-05 phen CRABP2 17 36968710 MED1 1:243544827 rs113435706 0.000245581713543445 phen MED1 16 68335392 NFATC3 1:243544827 rs11350 0.000113774081315591 phen NFATC3 6 15195682 DTNBP1 1:243544827 rs113532504 4.24E-06 phen DTNBP1 8 101765988 RNF19A 1:243544827 rs113657091 1.88E-07 phen RNF19A 3 122036822 CSTA 1:243544827 rs113686831 5.27E-06 phen CSTA 4 39804616 HIP2 1:243544827 rs113769228 6.79E-05 phen HIP2 21 34609596 IFNAR2 1:243544827 rs1137779 4.03E-06 phen IFNAR2 6 32502901 PPT2 1:243544827 rs113787140 0.000271192567216334 phen PPT2 5 142500512 ARHGAP26 1:243544827 rs113801037 9.05E-05 phen ARHGAP26 2 224832136 WDFY1 1:243544827 rs1138616 2.56E-11 phen WDFY1 12 286481 SLC6A13 1:243544827 rs113879277 8.96E-05 phen SLC6A13 6 29832919 HCG9 1:243544827 rs113959448 1.22E-19 phen HCG9 6 31438243 HCP5 1:243544827 rs114034067 0.000203962063658625 phen HCP5 6 30461085 HLA-E 1:243544827 rs114114145 2.05E-07 phen HLA-E 19 33146637 ANKRD27 1:243544827 rs114559145 4.85E-07 phen ANKRD27 6 31667028 EHMT2 1:243544827 rs114627445 2.99E-05 phen EHMT2 5 156987250 ADAM19 1:243544827 rs11465272 3.42E-05 phen ADAM19 5 11032162 ??? 1:243544827 rs114717582 0.000105806056433898 phen ??? 1 174114873 CACYBP 1:243544827 rs1147980 8.07E-05 phen CACYBP 6 31436273 C6orf48 1:243544827 rs114808309 9.83E-05 phen C6orf48 6 33298478 TAPBP 1:243544827 rs114850779 2.32E-07 phen TAPBP 9 93504263 NFIL3 1:243544827 rs1148848 0.000162858098649641 phen NFIL3 1 150930926 ARNT 1:243544827 rs114908993 3.47E-05 phen ARNT 6 13197441 PHACTR1 1:243544827 rs1150598 3.89E-15 phen PHACTR1 7 12261911 TMEM106B 1:243544827 rs11509880 2.20E-10 phen TMEM106B 7 12261911 TMEM106B 1:243544827 rs11509880 3.55E-09 phen TMEM106B 20 62374219 ZGPAT 1:243544827 rs1151626 0.000104982042228872 phen ZGPAT 6 32146657 AIF1 1:243544827 rs115186377 1.08E-07 phen AIF1 9 34162533 UBAP1 1:243544827 rs11521438 6.67E-05 phen UBAP1 14 56945549 NAT12 1:243544827 rs1152547 8.47E-05 phen NAT12 6 30990306 CLIC1 1:243544827 rs115268471 1.18E-05 phen CLIC1 6 29906044 GABBR1 1:243544827 rs115317940 3.85E-06 phen GABBR1 15 45663193 SPATA5L1 1:243544827 rs1153854 2.68E-22 phen SPATA5L1 7 154720259 LOC100132707 1:243544827 rs11543936 3.83E-06 phen LOC100132707 2 85843348 USP39 1:243544827 rs11544042 9.30E-21 phen USP39 12 6602696 VAMP1 1:243544827 rs11545055 5.27E-15 phen VAMP1 19 36246418 U2AF1L4 1:243544827 rs11549030 6.77E-10 phen U2AF1L4 6 31440415 LTA 1:243544827 rs115524885 3.08E-05 phen LTA 17 7462555 TNFSF12 1:243544827 rs11552708 3.29E-09 phen TNFSF12 6 32428397 LOC642073 1:243544827 rs115546460 1.11E-18 phen LOC642073 2 63328774 OTX1 1:243544827 rs115634863 1.50E-09 phen OTX1 7 108011965 CBLL1 1:243544827 rs1156502 0.000129549948192201 phen CBLL1 1 227189642 PSEN2 1:243544827 rs11578103 0.000108361625367859 phen PSEN2 1 161930954 B4GALT3 1:243544827 rs11579627 3.36E-05 phen B4GALT3 9 140413317 C9orf75 1:243544827 rs115803884 0.000261272532836164 phen C9orf75 1 43302515 ERMAP 1:243544827 rs11581978 8.23E-11 phen ERMAP 1 150694777 CTSS 1:243544827 rs11583636 1.02E-09 phen CTSS 1 46656964 UQCRH 1:243544827 rs11584024 2.92E-08 phen UQCRH 1 205034723 NUAK2 1:243544827 rs11588412 7.76E-06 phen NUAK2 1 78575849 USP33 1:243544827 rs11589864 0.000213276803807025 phen USP33 1 207955963 IL20 1:243544827 rs115906510 2.85E-05 phen IL20 10 27821004 RAB18 1:243544827 rs11598492 0.000266826167729231 phen RAB18 11 196944 BET1L 1:243544827 rs11604127 3.66E-06 phen BET1L 11 47725306 MYBPC3 1:243544827 rs11604825 5.44E-09 phen MYBPC3 11 75055107 ARRB1 1:243544827 rs11604864 8.58E-05 phen ARRB1 11 129718478 NFRKB 1:243544827 rs11607337 0.000272910886026419 phen NFRKB 11 62210081 B3GAT3 1:243544827 rs11607566 0.000197821988179421 phen B3GAT3 6 32638146 GPSM3 1:243544827 rs116081545 0.000160755177393362 phen GPSM3 12 29920088 TMTC1 1:243544827 rs11609828 1.74E-14 phen TMTC1 12 125494940 BRI3BP 1:243544827 rs11614174 9.08E-05 phen BRI3BP 12 33019436 C12orf35 1:243544827 rs11615313 2.51E-05 phen C12orf35 9 132613008 FNBP1 1:243544827 rs116214654 6.11E-07 phen FNBP1 14 76470655 C14orf118 1:243544827 rs11623313 0.000164176117100563 phen C14orf118 4 76826582 NAAA 1:243544827 rs116248809 4.86E-16 phen NAAA 14 21347911 RNASE2 1:243544827 rs11626267 4.14E-05 phen RNASE2 14 90968808 CCDC88C 1:243544827 rs11628344 0.000137822895800724 phen CCDC88C 14 24844054 GMPR2 1:243544827 rs11628929 0.000177690090615231 phen GMPR2 15 76608686 ETFA 1:243544827 rs11631423 2.45E-07 phen ETFA 6 31678028 LY6G5C 1:243544827 rs116336999 1.12E-13 phen LY6G5C 6 26208269 ??? 1:243544827 rs116337444 5.43E-27 phen ??? 6 31445771 MICB 1:243544827 rs116345750 2.41E-16 phen MICB 15 75088962 CSK 1:243544827 rs11635664 1.10E-09 phen CSK 15 90882643 IDH2 1:243544827 rs11638227 0.000178232994194828 phen IDH2

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[selimkal]

Hi Jim,

I was wondering if you had a chance to take a look into this?

Thanks!

Best, Selim

2017-04-13 15:45 GMT-04:00 Jim Robinson notifications@github.com:

Sorry no, I'm traveling, will see next week.

2017-04-13 14:38 GMT-04:00 selimkal notifications@github.com:

Hi,

Any progress/feedback on this by any chance?

Thanks!

---------- Forwarded message ---------- From: Selim Kalayci skalayci@gmail.com Date: Mon, Apr 10, 2017 at 4:22 PM Subject: Re: [igvteam/igv] popup window is not opening up in igv.js beta version for gwas track (#385) To: igvteam/igv < reply@reply.github.com

Cc: igvteam/igv igv@noreply.github.com, Author < author@noreply.github.com>

Hi Jim,

I see, good to know about the flat-files/web-service support. And yes, I had seen the usage of flat files for eqtl data in one of the (rather old) test pages I believe.

Attached please find a sample eqtl flat file (please note that some columns are simply placeholders, added just to make it work in browser).

And here is the loadTrack snippet I use in the html:

igv.browser.loadTrack({ url: './data/tes-cis-eqtl.txt', name: 'test', format: 'gtexGWAS',

featureType: 'gwas', colorScale: { thresholds: [], colors:['rgb(122,179,23)'] },

maxLogP: 16, height: 150, label: 'Test'}); }

Hope this would help.

Thanks!

On Thu, Apr 6, 2017 at 11:38 AM, Jim Robinson notifications@github.com wrote:

OK, that is helpful. Its a bit fortunate this is working at all for you, the flat eqtl files originally supported the gtex portal (thus gtex in the name). However the portal now uses a webservice, as you note, and the eqtl flat files are not supported or tested anymore. I supposed you discovered this format from browsing the source code. Could you provide a small test file, and also a sample web page or track config javascript snippet that uses it?

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SNP_Chr SNP_Pos_hg19 Transcript_GeneSymbol 1:243544827 Rs_ID P-val phen Gene 1 28225114 RPA2 1:243544827 rs1000431 1.45E-18 phen RPA2 4 1324346 CRIPAK 1:243544827 rs10012416 1.43E-14 phen CRIPAK 4 84167984 HPSE 1:243544827 rs10014278 3.19E-05 phen HPSE 4 2862190 MFSD10 1:243544827 rs10026792 7.53E-05 phen MFSD10 4 88292147 HSD17B11 1:243544827 rs10034537 0.000147690179652976 phen HSD17B11 5 176484984 MXD3 1:243544827 rs10035183 0.000101460925956596 phen MXD3 5 95990869 CAST 1:243544827 rs10039522 6.90E-08 phen CAST 12 129625269 SLC15A4 1:243544827 rs10047656 0.00024678557764908 phen SLC15A4 5 176735187 RAB24 1:243544827 rs10051822 0.000109593885762883 phen RAB24 5 35512003 BRIX1 1:243544827 rs10065345 0.000108780888918509 phen BRIX1 5 75803002 PDE8B 1:243544827 rs10066611 0.000136411934082815 phen PDE8B 5 179050918 HNRNPH1 1:243544827 rs10066669 9.47E-08 phen HNRNPH1 5 150123251 C5orf62 1:243544827 rs10068228 6.19E-05 phen C5orf62 5 147547917 FBXO38 1:243544827 rs10068916 2.03E-06 phen FBXO38 5 95990057 CAST 1:243544827 rs10075736 6.04E-13 phen CAST 15 90799802 NGRN 1:243544827 rs10083710 0.000151023197346242 phen NGRN 8 131420688 ASAP1 1:243544827 rs10086773 0.000129773412059186 phen ASAP1 8 28909523 HMBOX1 1:243544827 rs10088428 8.92E-10 phen HMBOX1 8 41234902 GOLGA7 1:243544827 rs10088901 5.14E-05 phen GOLGA7 8 3165777 ??? 1:243544827 rs10091831 0.000122948939352581 phen ??? 5 149492119 DCTN4 1:243544827 rs1009424 0.00023937918604321 phen DCTN4 8 23324877 ENTPD4 1:243544827 rs10094683 1.09E-10 phen ENTPD4 19 48702219 CARD8 1:243544827 rs1010089 7.17E-19 phen CARD8 8 6793006 DEFA4 1:243544827 rs10103091 6.89E-06 phen DEFA4 8 145004944 PLEC1 1:243544827 rs10107388 5.85E-06 phen PLEC1 8 81791762 TPD52 1:243544827 rs10112204 0.000159993599405168 phen TPD52 9 103065265 INVS 1:243544827 rs10124893 2.83E-06 phen INVS 14 21274036 RPGRIP1 1:243544827 rs10131805 6.67E-05 phen RPGRIP1 14 93148543 BTBD7 1:243544827 rs10139162 2.58E-05 phen BTBD7 14 93693604 UBR7 1:243544827 rs10144530 2.83E-05 phen UBR7 14 24899194 KHNYN 1:243544827 rs10146759 5.31E-13 phen KHNYN 14 100838007 SLC25A29 1:243544827 rs10149239 9.30E-14 phen SLC25A29 14 78380965 ADCK1 1:243544827 rs10150472 5.44E-12 phen ADCK1 9 96345328 FAM120AOS 1:243544827 rs10156602 0.000148145375061101 phen FAM120AOS 11 65667149 MUS81 1:243544827 rs10160792 3.08E-06 phen MUS81 18 9542084 PPP4R1 1:243544827 rs10163801 1.66E-05 phen PPP4R1 12 108949966 ISCU 1:243544827 rs1016881 9.13E-14 phen ISCU 2 30449594 LBH 1:243544827 rs10175798 7.77E-08 phen LBH 2 48994107 CCDC128 1:243544827 rs10176937 0.000119569297541119 phen CCDC128 2 85524876 TGOLN2 1:243544827 rs10178604 9.69E-05 phen TGOLN2 2 88949205 RPIA 1:243544827 rs10178815 0.000182640507008978 phen RPIA 2 160427646 BAZ2B 1:243544827 rs10202187 3.79E-13 phen BAZ2B 2 201806597 CASP8 1:243544827 rs10207973 6.55E-05 phen CASP8 2 100075804 REV1 1:243544827 rs10207981 1.27E-05 phen REV1 12 26569724 SSPN 1:243544827 rs1021296 0.000126647925312339 phen SSPN 4 88291760 HSD17B11 1:243544827 rs10213098 0.000260699941189299 phen HSD17B11 4 4864276 LYAR 1:243544827 rs10213148 4.81E-05 phen LYAR 4 175632850 GPM6A 1:243544827 rs10213402 0.000157278996774258 phen GPM6A 7 128599397 IRF5 1:243544827 rs10229001 6.36E-32 phen IRF5 7 128599397 IRF5 1:243544827 rs10229001 7.93E-15 phen IRF5 7 97785669 TECPR1 1:243544827 rs10243469 1.81E-05 phen TECPR1 7 140936088 KIAA1147 1:243544827 rs1024722 0.000197813722609637 phen KIAA1147 7 102022586 LRWD1 1:243544827 rs10249581 6.46E-14 phen LRWD1 7 44584551 ??? 1:243544827 rs10260606 5.52E-05 phen ??? 11 3865786 TRIM68 1:243544827 rs1026231 5.28E-05 phen TRIM68 7 38636891 GPR141 1:243544827 rs10263645 0.00020568202311997 phen GPR141 7 30731993 FAM188B 1:243544827 rs10271601 4.81E-05 phen FAM188B 8 144107977 LY6E 1:243544827 rs10283236 1.05E-08 phen LY6E 9 125157198 PTGS1 1:243544827 rs10306194 6.51E-05 phen PTGS1 4 102223386 FLJ20021 1:243544827 rs1031034 5.81E-13 phen FLJ20021 8 9040858 PPP1R3B 1:243544827 rs1038248 0.000244494555920015 phen PPP1R3B 5 73927752 ENC1 1:243544827 rs1039320 1.66E-32 phen ENC1 5 73927752 HEXB 1:243544827 rs1039320 5.94E-06 phen HEXB 1 203156080 MYBPH 1:243544827 rs10399931 1.68E-17 phen MYBPH 6 111902079 TRAF3IP2 1:243544827 rs1040382 1.48E-08 phen TRAF3IP2 19 40777133 PLD3 1:243544827 rs10405207 0.000143339270974138 phen PLD3 19 45011727 ZNF234 1:243544827 rs10408058 2.87E-05 phen ZNF234 19 20782523 ZNF431 1:243544827 rs10411545 2.02E-05 phen ZNF431 19 43202770 LYPD3 1:243544827 rs10412221 5.34E-05 phen LYPD3 19 2575186 REXO1 1:243544827 rs10419362 0.000118265964613741 phen REXO1 19 42125660 CEACAM4 1:243544827 rs1041994 1.00E-19 phen CEACAM4 19 19383537 KIAA0892 1:243544827 rs10419998 9.62E-16 phen KIAA0892 19 49390878 DHDH 1:243544827 rs10423931 9.19E-05 phen DHDH 5 137902339 PAIP2 1:243544827 rs1042665 3.39E-05 phen PAIP2 6 43753212 ZNF318 1:243544827 rs10434 0.000138460768708134 phen ZNF318 22 42981678 NDUFA6 1:243544827 rs1043606 0.000176163164189338 phen NDUFA6 19 15708779 CYP4F3 1:243544827 rs10439166 0.000157463896249393 phen CYP4F3 2 203055522 CASP8 1:243544827 rs10445793 6.04E-05 phen CASP8 8 17917428 ASAH1 1:243544827 rs10448131 5.10E-11 phen ASAH1 5 132752323 SKP1 1:243544827 rs10452539 0.000283362981110264 phen SKP1 8 142200467 DENND3 1:243544827 rs1045303 2.54E-07 phen DENND3 11 20265876 ??? 1:243544827 rs10458881 0.000246625051048321 phen ??? 19 1095514 GPX4 1:243544827 rs1046040 5.99E-07 phen GPX4 1 22443887 HSPC157 1:243544827 rs1046310 9.80E-11 phen HSPC157 2 74699778 MRPL53 1:243544827 rs1047911 1.98E-05 phen MRPL53 7 73108924 WBSCR22 1:243544827 rs10479665 1.46E-11 phen WBSCR22 1 182542851 RNASEL 1:243544827 rs1048260 3.49E-05 phen RNASEL 6 38979441 C6orf64 1:243544827 rs10484850 7.00E-05 phen C6orf64 10 112053599 SMNDC1 1:243544827 rs1050755 9.51E-07 phen SMNDC1 7 100782460 GNB2 1:243544827 rs1050955 9.57E-05 phen GNB2 5 51955408 PELO 1:243544827 rs10512980 0.000151368076302287 phen PELO 9 111881856 C9orf6 1:243544827 rs1051474 1.18E-05 phen C9orf6 3 127391378 ABTB1 1:243544827 rs1056235 2.03E-07 phen ABTB1 20 7962128 TMX4 1:243544827 rs1058007 4.53E-09 phen TMX4 13 52319678 DHRS12 1:243544827 rs1060562 2.13E-05 phen DHRS12 10 100189138 HPS1 1:243544827 rs1061135 0.000247364364585373 phen HPS1 19 1086211 POLR2E 1:243544827 rs1061233 0.000265642859180972 phen POLR2E 9 135764081 C9orf9 1:243544827 rs1062218 0.000120073510332433 phen C9orf9 7 87835469 SRI 1:243544827 rs1063964 1.59E-05 phen SRI 15 45981317 SQRDL 1:243544827 rs10643 1.63E-08 phen SQRDL 6 32546615 NCR3 1:243544827 rs1064717 8.69E-05 phen NCR3 16 1839134 NME3 1:243544827 rs1065666 5.96E-05 phen NME3 12 1947193 ADIPOR2 1:243544827 rs10735004 2.84E-05 phen ADIPOR2 9 75991893 ANXA1 1:243544827 rs10735622 3.68E-10 phen ANXA1 12 41800488 PPHLN1 1:243544827 rs10735993 0.000262163983886547 phen PPHLN1 14 94353093 MOAP1 1:243544827 rs1073778 6.25E-05 phen MOAP1 9 124021025 GSN 1:243544827 rs10739593 1.04E-07 phen GSN 12 124231355 ATP6V0A2 1:243544827 rs10744161 1.21E-05 phen ATP6V0A2 12 97871380 NEDD1 1:243544827 rs10745798 5.54E-05 phen NEDD1 1 213050209 LQK1 1:243544827 rs10746439 2.50E-16 phen LQK1 12 56077418 BAZ2A 1:243544827 rs10747759 0.000113075797205558 phen BAZ2A 10 101283330 BLOC1S2 1:243544827 rs10748781 8.55E-05 phen BLOC1S2 1 168166616 TIPRL 1:243544827 rs10753766 2.62E-08 phen TIPRL 8 21762915 XPO7 1:243544827 rs1075417 1.88E-05 phen XPO7 9 35776190 GBA2 1:243544827 rs10758322 3.28E-06 phen GBA2 9 104623299 RNF20 1:243544827 rs10760813 5.50E-05 phen RNF20 10 71040106 HNRPH3 1:243544827 rs10762273 0.000163874357199423 phen HNRPH3 11 3914033 STIM1 1:243544827 rs10767685 1.10E-06 phen STIM1 6 36348689 ETV7 1:243544827 rs1076928 6.03E-10 phen ETV7 12 10215582 CLEC9A 1:243544827 rs10772230 9.05E-08 phen CLEC9A 12 10492728 KLRC3 1:243544827 rs10772261 0.000101338522546955 phen KLRC3 12 6242259 VWF 1:243544827 rs10774396 3.75E-14 phen VWF 15 58723426 AQP9 1:243544827 rs1077835 0.000257243207454436 phen AQP9 12 109133588 CORO1C 1:243544827 rs10778656 1.05E-09 phen CORO1C 9 78242109 PCSK5 1:243544827 rs10781300 3.77E-07 phen PCSK5 12 53847473 C12orf10 1:243544827 rs10783580 3.39E-06 phen C12orf10 11 65363865 KAT5 1:243544827 rs10791819 0.000200902878356274 phen KAT5 11 65363865 MAP3K11 1:243544827 rs10791819 3.62E-08 phen MAP3K11 10 7319541 PRKCQ 1:243544827 rs10795539 5.89E-05 phen PRKCQ 1 156735422 C1orf66 1:243544827 rs10796965 0.000149363309105606 phen C1orf66 1 160497984 CD84 1:243544827 rs10797073 1.32E-05 phen CD84 1 182373498 GLUL 1:243544827 rs10797773 6.03E-05 phen GLUL 1 185394834 IVNS1ABP 1:243544827 rs10798014 0.000108398870819528 phen IVNS1ABP 1 33941028 S100PBP 1:243544827 rs10798954 0.000116535220277128 phen S100PBP 1 200508928 CSRP1 1:243544827 rs10800707 0.000278059142334148 phen CSRP1 1 236311886 GPR137B 1:243544827 rs10802285 0.000182938541798671 phen GPR137B 1 236771229 LGALS8 1:243544827 rs10802552 1.30E-07 phen LGALS8 1 15278473 KIAA1026 1:243544827 rs10803327 2.27E-14 phen KIAA1026 7 151633265 GALNT11 1:243544827 rs10807990 2.53E-07 phen GALNT11 7 107552088 BCAP29 1:243544827 rs10808155 7.55E-05 phen BCAP29 1 93854688 DR1 1:243544827 rs1081521 1.81E-10 phen DR1 9 123572038 LOC253039 1:243544827 rs10818476 7.86E-26 phen LOC253039 9 125002275 RBM18 1:243544827 rs10818655 9.36E-05 phen RBM18 10 72064976 TYSND1 1:243544827 rs10823515 9.17E-06 phen TYSND1 10 75464853 SEC24C 1:243544827 rs10824028 4.82E-05 phen SEC24C 11 93370692 C11orf54 1:243544827 rs10831080 0.000202388805446248 phen C11orf54 11 93421782 SNORA25 1:243544827 rs10831093 2.13E-11 phen SNORA25 11 2927670 SLC22A18AS 1:243544827 rs10832888 0.00027600042102939 phen SLC22A18AS 11 7606498 PPFIBP2 1:243544827 rs10839816 2.53E-09 phen PPFIBP2 11 8736695 TRIM66 1:243544827 rs10840114 1.88E-09 phen TRIM66 12 9935825 GABARAPL1 1:243544827 rs10844782 0.000133040249207915 phen GABARAPL1 12 7900184 CLEC4C 1:243544827 rs10845821 2.31E-35 phen CLEC4C 12 131295828 STX2 1:243544827 rs10848208 3.07E-09 phen STX2 12 6412036 PTMS 1:243544827 rs10849438 0.000233577606674428 phen PTMS 12 6654050 HOM-TES-103 1:243544827 rs10849488 3.33E-11 phen HOM-TES-103 15 63100467 RAB8B 1:243544827 rs10851718 7.08E-05 phen RAB8B 1 111733724 CEPT1 1:243544827 rs10857859 8.63E-05 phen CEPT1 9 137857863 FCN1 1:243544827 rs10858304 1.28E-09 phen FCN1 12 92956190 MRPL42 1:243544827 rs10859340 0.000270303041652793 phen MRPL42 12 102293288 DRAM1 1:243544827 rs10860815 5.86E-09 phen DRAM1 1 219260673 LYPLAL1 1:243544827 rs10863423 4.68E-09 phen LYPLAL1 3 49858142 UBA7 1:243544827 rs10865958 8.80E-18 phen UBA7 8 23468924 NKX3-1 1:243544827 rs10866831 1.36E-21 phen NKX3-1 9 140534584 ARRDC1 1:243544827 rs10867035 5.35E-05 phen ARRDC1 9 72313481 PTAR1 1:243544827 rs10867922 1.26E-08 phen PTAR1 9 140006491 MAN1B1 1:243544827 rs10870180 7.00E-09 phen MAN1B1 14 23217371 RBM23 1:243544827 rs10873040 1.57E-05 phen RBM23 12 49012011 C12orf41 1:243544827 rs10875848 1.01E-06 phen C12orf41 12 56050706 DGKA 1:243544827 rs10876844 0.000261124760584804 phen DGKA 3 4114156 TRNT1 1:243544827 rs1087823 5.52E-05 phen TRNT1 12 66872341 HMGA2 1:243544827 rs10878433 0.000158212696704638 phen HMGA2 12 46595290 SLC38A1 1:243544827 rs10880935 0.000226174929538926 phen SLC38A1 10 104973061 C10orf32 1:243544827 rs10883848 6.45E-06 phen C10orf32 1 151068637 CDC42SE1 1:243544827 rs10888404 1.04E-05 phen CDC42SE1 1 153171148 SPRR2D 1:243544827 rs10888535 0.000249047422175854 phen SPRR2D 11 126425577 ST3GAL4 1:243544827 rs10893539 3.55E-05 phen ST3GAL4 11 129698856 TMEM45B 1:243544827 rs10894147 1.76E-18 phen TMEM45B 11 72700779 ATG16L2 1:243544827 rs10898894 0.000204941336870698 phen ATG16L2 11 76600932 PHCA 1:243544827 rs10899303 8.40E-11 phen PHCA 11 960641 RIC8A 1:243544827 rs10902251 1.57E-05 phen RIC8A 1 26666196 AIM1L 1:243544827 rs10902740 2.46E-05 phen AIM1L 10 5541181 RBM17 1:243544827 rs10904516 2.13E-05 phen RBM17 1 154710904 HAX1 1:243544827 rs10908429 7.85E-05 phen HAX1 1 161008535 TSTD1 1:243544827 rs10908821 3.87E-18 phen TSTD1 1 161008535 TSTD1 1:243544827 rs10908821 7.19E-06 phen TSTD1 1 181493767 CACNA1E 1:243544827 rs10910948 8.34E-05 phen CACNA1E 1 183489203 SMG7 1:243544827 rs10911353 7.15E-17 phen SMG7 3 126212567 ZXDC 1:243544827 rs1091553 2.37E-08 phen ZXDC 1 24085063 FUCA1 1:243544827 rs10917423 5.61E-10 phen FUCA1 1 19756869 CAPZB 1:243544827 rs10917449 2.77E-06 phen CAPZB 16 10829280 TXNDC11 1:243544827 rs1091849 0.000186756450729357 phen TXNDC11 2 15737268 DDX1 1:243544827 rs10929377 2.24E-19 phen DDX1 2 10558066 HPCAL1 1:243544827 rs10929663 9.46E-07 phen HPCAL1 6 89569254 RNGTT 1:243544827 rs10944411 2.49E-07 phen RNGTT 7 6541015 AIMP2 1:243544827 rs10951985 0.000137026687318167 phen AIMP2 8 124782340 MTSS1 1:243544827 rs10956148 0.000130050395073069 phen MTSS1 8 38052482 LSM1 1:243544827 rs10958541 2.46E-20 phen LSM1 8 39798341 IDO1 1:243544827 rs10958575 7.76E-06 phen IDO1 9 34151280 NUDT2 1:243544827 rs10971956 1.98E-13 phen NUDT2 9 5433404 JAK2 1:243544827 rs10975114 5.85E-05 phen JAK2 9 100736718 ??? 1:243544827 rs10984599 9.83E-05 phen ??? 9 130611523 C9orf114 1:243544827 rs10987756 0.000171917748382816 phen C9orf114 9 133014623 LOC158301 1:243544827 rs10988658 0.000132175255094301 phen LOC158301 9 95551617 BICD2 1:243544827 rs10992469 1.55E-07 phen BICD2 9 97058302 HIATL1 1:243544827 rs10993151 2.23E-20 phen HIATL1 10 51563993 TIMM23 1:243544827 rs10994675 6.96E-07 phen TIMM23 10 69602892 SIRT1 1:243544827 rs10997828 7.43E-21 phen SIRT1 10 70386834 SUPV3L1 1:243544827 rs10998342 0.000189582196576523 phen SUPV3L1 10 71043781 HNRNPH3 1:243544827 rs10998696 0.00013570880175954 phen HNRNPH3 10 72174390 EIF4EBP2 1:243544827 rs10999323 1.44E-05 phen EIF4EBP2 10 52357891 SGMS1 1:243544827 rs11006259 9.81E-05 phen SGMS1 10 20414564 PLXDC2 1:243544827 rs11011813 0.000192000641223335 phen PLXDC2 10 26706338 YME1L1 1:243544827 rs11015094 0.000269542672528715 phen YME1L1 10 129892160 PTPRE 1:243544827 rs11016068 0.000126519194155101 phen PTPRE 11 29781464 C11orf46 1:243544827 rs11030799 6.74E-05 phen C11orf46 11 32459923 EIF3M 1:243544827 rs11031783 0.000183477239207002 phen EIF3M 11 44723871 CD82 1:243544827 rs11038116 1.44E-05 phen CD82 12 22666996 KIAA0528 1:243544827 rs11046453 0.000102487309033307 phen KIAA0528 12 25051596 BCAT1 1:243544827 rs11047695 5.97E-12 phen BCAT1 4 185304463 IRF2 1:243544827 rs1105207 0.000177850007418945 phen IRF2 1 2141985 C1orf86 1:243544827 rs1105269 2.15E-07 phen C1orf86 12 10283711 CLEC7A 1:243544827 rs11053624 2.10E-06 phen CLEC7A 12 7904111 CLEC4C 1:243544827 rs11055602 5.35E-29 phen CLEC4C 12 123770362 CDK2AP1 1:243544827 rs11057242 1.85E-16 phen CDK2AP1 12 123219785 DENR 1:243544827 rs11059650 1.47E-05 phen DENR 12 6241707 CD9 1:243544827 rs11064041 4.15E-12 phen CD9 12 6705937 NOP2 1:243544827 rs11064275 0.000182335686654493 phen NOP2 13 111172407 RAB20 1:243544827 rs11069851 9.42E-08 phen RAB20 16 25039449 ARHGAP17 1:243544827 rs11074668 9.16E-13 phen ARHGAP17 17 18664378 FLII 1:243544827 rs11078420 1.94E-05 phen FLII 17 3820239 P2RX1 1:243544827 rs11078476 7.12E-24 phen P2RX1 17 40545770 VAT1 1:243544827 rs11079043 9.76E-05 phen VAT1 18 44659001 HDHD2 1:243544827 rs11082563 0.000147466205368872 phen HDHD2 19 3735215 EEF2 1:243544827 rs11085038 0.000173248314549518 phen EEF2 19 9546460 ZNF266 1:243544827 rs11086035 1.17E-11 phen ZNF266 19 9546460 ZNF266 1:243544827 rs11086035 5.88E-21 phen ZNF266 14 20849002 FLJ10357 1:243544827 rs1108614 0.000228205532379093 phen FLJ10357 21 19070092 C21orf91 1:243544827 rs11088649 5.14E-05 phen C21orf91 4 37375277 TBC1D1 1:243544827 rs11096872 6.04E-05 phen TBC1D1 4 100744401 DAPP1 1:243544827 rs11097677 5.13E-05 phen DAPP1 4 159857539 RAPGEF2 1:243544827 rs11100203 1.13E-08 phen RAPGEF2 1 111427656 KCND3 1:243544827 rs11102172 0.000125172667347624 phen KCND3 9 138980277 NACC2 1:243544827 rs11103323 1.56E-07 phen NACC2 12 104192793 NT5DC3 1:243544827 rs11111790 2.21E-05 phen NT5DC3 1 219280033 LYPLAL1 1:243544827 rs11118215 3.93E-08 phen LYPLAL1 1 209938987 TRAF3IP3 1:243544827 rs11119339 9.68E-14 phen TRAF3IP3 1 212955231 NSL1 1:243544827 rs11120025 1.68E-07 phen NSL1 1 10455148 KIF1B 1:243544827 rs11121559 2.29E-07 phen KIF1B 1 231111477 TTC13 1:243544827 rs11122172 4.52E-17 phen TTC13 1 231111477 TTC13 1:243544827 rs11122172 5.20E-15 phen TTC13 2 99884546 MITD1 1:243544827 rs11123777 7.87E-05 phen MITD1 2 3471146 TTC15 1:243544827 rs11127428 9.82E-12 phen TTC15 3 9836312 TADA3 1:243544827 rs11131186 0.000135748205918201 phen TADA3 13 77434603 KCTD12 1:243544827 rs1113312 5.71E-05 phen KCTD12 5 175904141 RNF44 1:243544827 rs11134977 9.98E-06 phen RNF44 9 140380376 FBXW5 1:243544827 rs11137268 4.42E-05 phen FBXW5 6 6810109 F13A1 1:243544827 rs111418267 0.000120255308965732 phen F13A1 9 71184184 PIP5K1B 1:243544827 rs11142965 5.93E-05 phen PIP5K1B 19 876882 CFD 1:243544827 rs111469573 1.24E-08 phen CFD 12 133385721 GOLGA3 1:243544827 rs11147084 4.28E-05 phen GOLGA3 17 259648 C17orf97 1:243544827 rs11150882 1.08E-29 phen C17orf97 17 259648 C17orf97 1:243544827 rs11150882 6.72E-32 phen C17orf97 15 42323272 NUSAP1 1:243544827 rs111532177 0.000245297284230151 phen NUSAP1 6 139099401 CCDC28A 1:243544827 rs11155000 3.79E-05 phen CCDC28A 1 76394910 RABGGTB 1:243544827 rs11161905 3.24E-05 phen RABGGTB 3 134834409 PPP2R3A 1:243544827 rs111621177 1.46E-05 phen PPP2R3A 12 51117593 DIP2B 1:243544827 rs11169530 8.10E-06 phen DIP2B 12 57287522 DCTN2 1:243544827 rs11172038 0.000281833966792196 phen DCTN2 16 1294883 FAM173A 1:243544827 rs111743119 6.02E-05 phen FAM173A 12 62530388 FAM19A2 1:243544827 rs11174342 0.000123227868694894 phen FAM19A2 17 76901058 TIMP2 1:243544827 rs111770145 5.35E-07 phen TIMP2 12 69175793 MDM2 1:243544827 rs11177370 1.10E-05 phen MDM2 12 69175793 SLC35E3 1:243544827 rs11177370 3.30E-09 phen SLC35E3 12 69769275 YEATS4 1:243544827 rs11177631 2.57E-10 phen YEATS4 19 2191796 GNA15 1:243544827 rs111785160 3.45E-05 phen GNA15 12 43405540 YAF2 1:243544827 rs11181845 2.00E-05 phen YAF2 12 47719326 LOC728181 1:243544827 rs11183849 0.000152601059473514 phen LOC728181 20 3052586 SPEF1 1:243544827 rs111869749 7.96E-05 phen SPEF1 8 39816912 INDO 1:243544827 rs111880438 9.26E-05 phen INDO 10 99159096 FRAT1 1:243544827 rs11189203 1.97E-09 phen FRAT1 10 99181008 FRAT2 1:243544827 rs11189214 4.80E-07 phen FRAT2 10 101185830 CHUK 1:243544827 rs11190087 0.000111001703485336 phen CHUK 10 105170649 USMG5 1:243544827 rs11191683 6.63E-43 phen USMG5 10 105245352 C10orf78 1:243544827 rs11191711 0.000190512694944968 phen C10orf78 10 112013274 ??? 1:243544827 rs11195048 0.000129987667599754 phen ??? 10 81931780 ANXA11 1:243544827 rs11201966 9.60E-09 phen ANXA11 10 89895807 ??? 1:243544827 rs11202661 0.000132855090039766 phen ??? 16 88827338 CDK10 1:243544827 rs112028717 7.20E-08 phen CDK10 10 91213935 FAS 1:243544827 rs11203134 6.61E-05 phen FAS 1 151793174 FAM63A 1:243544827 rs11204894 0.000166263169282398 phen FAM63A 1 44474802 CCDC24 1:243544827 rs11210939 1.61E-18 phen CCDC24 1 44541961 MED8 1:243544827 rs11210951 8.22E-06 phen MED8 1 48016189 CMPK1 1:243544827 rs11211551 0.000272660865474489 phen CMPK1 11 108053887 ATM 1:243544827 rs11212542 6.37E-13 phen ATM 11 86683231 ??? 1:243544827 rs112141754 3.61E-06 phen ??? 19 50047311 RCN3 1:243544827 rs112173908 3.44E-08 phen RCN3 20 60243836 OSBPL2 1:243544827 rs1122269 5.43E-05 phen OSBPL2 11 58589305 FAM111A 1:243544827 rs11229642 9.24E-06 phen FAM111A 17 46191032 SP6 1:243544827 rs112306902 8.85E-05 phen SP6 11 64046885 NUDT22 1:243544827 rs11231741 0.000188609303502628 phen NUDT22 10 35550294 CUL2 1:243544827 rs112355105 1.90E-07 phen CUL2 19 46310228 SYMPK 1:243544827 rs112400363 0.000209044895929256 phen SYMPK 2 127419105 GYPC 1:243544827 rs112403595 5.23E-07 phen GYPC 2 127419105 GYPC 1:243544827 rs112403595 5.52E-06 phen GYPC 9 134585181 RAPGEF1 1:243544827 rs11243480 2.68E-12 phen RAPGEF1 10 126323766 FAM53B 1:243544827 rs11245322 0.000239815785106628 phen FAM53B 5 176041931 B4GALT7 1:243544827 rs1124715 0.000220158407224203 phen B4GALT7 2 109042440 GCC2 1:243544827 rs112482682 0.000228421974579343 phen GCC2 10 124814481 ??? 1:243544827 rs11248371 3.21E-05 phen ??? 2 85094533 ST3GAL5 1:243544827 rs112524336 0.000254735041022514 phen ST3GAL5 10 12307894 ??? 1:243544827 rs11257655 1.27E-09 phen ??? 10 12307894 CAMK1D 1:243544827 rs11257655 8.55E-10 phen CAMK1D 10 12307894 CDC123 1:243544827 rs11257655 2.63E-07 phen CDC123 10 14534753 FAM107B 1:243544827 rs11259141 2.73E-06 phen FAM107B 17 34896877 GGNBP2 1:243544827 rs11263770 1.16E-09 phen GGNBP2 1 159976867 PIGM 1:243544827 rs11265305 0.000199657074809162 phen PIGM 16 1853335 HN1L 1:243544827 rs112690906 0.000232718015784108 phen HN1L 1 153779412 GATAD2B 1:243544827 rs1127091 4.61E-06 phen GATAD2B 19 40344366 ITPKC 1:243544827 rs112728066 0.00024888947935896 phen ITPKC 12 124559539 ??? 1:243544827 rs112745336 0.000130133078843364 phen ??? 3 183652932 ABCC5 1:243544827 rs112754234 2.89E-11 phen ABCC5 1 43443376 ELOVL1 1:243544827 rs112761111 0.000253321197068162 phen ELOVL1 11 32648203 PRRG4 1:243544827 rs112773089 1.70E-05 phen PRRG4 7 51091874 GRB10 1:243544827 rs112826922 1.80E-05 phen GRB10 17 40127060 AOC2 1:243544827 rs11296 0.000141658842773418 phen AOC2 7 100892196 CLDN15 1:243544827 rs112971669 8.58E-05 phen CLDN15 7 128755229 LOC286016 1:243544827 rs112984431 0.000157077350629057 phen LOC286016 1 33789968 PHC2 1:243544827 rs1130800 6.04E-06 phen PHC2 17 4637396 ZMYND15 1:243544827 rs1131456 2.42E-07 phen ZMYND15 4 102009720 PPP3CA 1:243544827 rs113159161 7.31E-05 phen PPP3CA 17 17145154 FLCN 1:243544827 rs113161761 4.48E-07 phen FLCN 12 7247395 C1RL 1:243544827 rs1132216 2.22E-07 phen C1RL 19 35919422 ALKBH6 1:243544827 rs113255036 6.96E-06 phen ALKBH6 6 31415150 LOC100129668 1:243544827 rs113286688 8.87E-06 phen LOC100129668 7 1133305 ZFAND2A 1:243544827 rs1133043 6.29E-08 phen ZFAND2A 1 156693135 CRABP2 1:243544827 rs1133856 6.35E-05 phen CRABP2 17 36968710 MED1 1:243544827 rs113435706 0.000245581713543445 phen MED1 16 68335392 NFATC3 1:243544827 rs11350 0.000113774081315591 phen NFATC3 6 15195682 DTNBP1 1:243544827 rs113532504 4.24E-06 phen DTNBP1 8 101765988 RNF19A 1:243544827 rs113657091 1.88E-07 phen RNF19A 3 122036822 CSTA 1:243544827 rs113686831 5.27E-06 phen CSTA 4 39804616 HIP2 1:243544827 rs113769228 6.79E-05 phen HIP2 21 34609596 IFNAR2 1:243544827 rs1137779 4.03E-06 phen IFNAR2 6 32502901 PPT2 1:243544827 rs113787140 0.000271192567216334 phen PPT2 5 142500512 ARHGAP26 1:243544827 rs113801037 9.05E-05 phen ARHGAP26 2 224832136 WDFY1 1:243544827 rs1138616 2.56E-11 phen WDFY1 12 286481 SLC6A13 1:243544827 rs113879277 8.96E-05 phen SLC6A13 6 29832919 HCG9 1:243544827 rs113959448 1.22E-19 phen HCG9 6 31438243 HCP5 1:243544827 rs114034067 0.000203962063658625 phen HCP5 6 30461085 HLA-E 1:243544827 rs114114145 2.05E-07 phen HLA-E 19 33146637 ANKRD27 1:243544827 rs114559145 4.85E-07 phen ANKRD27 6 31667028 EHMT2 1:243544827 rs114627445 2.99E-05 phen EHMT2 5 156987250 ADAM19 1:243544827 rs11465272 3.42E-05 phen ADAM19 5 11032162 ??? 1:243544827 rs114717582 0.000105806056433898 phen ??? 1 174114873 CACYBP 1:243544827 rs1147980 8.07E-05 phen CACYBP 6 31436273 C6orf48 1:243544827 rs114808309 9.83E-05 phen C6orf48 6 33298478 TAPBP 1:243544827 rs114850779 2.32E-07 phen TAPBP 9 93504263 NFIL3 1:243544827 rs1148848 0.000162858098649641 phen NFIL3 1 150930926 ARNT 1:243544827 rs114908993 3.47E-05 phen ARNT 6 13197441 PHACTR1 1:243544827 rs1150598 3.89E-15 phen PHACTR1 7 12261911 TMEM106B 1:243544827 rs11509880 2.20E-10 phen TMEM106B 7 12261911 TMEM106B 1:243544827 rs11509880 3.55E-09 phen TMEM106B 20 62374219 ZGPAT 1:243544827 rs1151626 0.000104982042228872 phen ZGPAT 6 32146657 AIF1 1:243544827 rs115186377 1.08E-07 phen AIF1 9 34162533 UBAP1 1:243544827 rs11521438 6.67E-05 phen UBAP1 14 56945549 NAT12 1:243544827 rs1152547 8.47E-05 phen NAT12 6 30990306 CLIC1 1:243544827 rs115268471 1.18E-05 phen CLIC1 6 29906044 GABBR1 1:243544827 rs115317940 3.85E-06 phen GABBR1 15 45663193 SPATA5L1 1:243544827 rs1153854 2.68E-22 phen SPATA5L1 7 154720259 LOC100132707 1:243544827 rs11543936 3.83E-06 phen LOC100132707 2 85843348 USP39 1:243544827 rs11544042 9.30E-21 phen USP39 12 6602696 VAMP1 1:243544827 rs11545055 5.27E-15 phen VAMP1 19 36246418 U2AF1L4 1:243544827 rs11549030 6.77E-10 phen U2AF1L4 6 31440415 LTA 1:243544827 rs115524885 3.08E-05 phen LTA 17 7462555 TNFSF12 1:243544827 rs11552708 3.29E-09 phen TNFSF12 6 32428397 LOC642073 1:243544827 rs115546460 1.11E-18 phen LOC642073 2 63328774 OTX1 1:243544827 rs115634863 1.50E-09 phen OTX1 7 108011965 CBLL1 1:243544827 rs1156502 0.000129549948192201 phen CBLL1 1 227189642 PSEN2 1:243544827 rs11578103 0.000108361625367859 phen PSEN2 1 161930954 B4GALT3 1:243544827 rs11579627 3.36E-05 phen B4GALT3 9 140413317 C9orf75 1:243544827 rs115803884 0.000261272532836164 phen C9orf75 1 43302515 ERMAP 1:243544827 rs11581978 8.23E-11 phen ERMAP 1 150694777 CTSS 1:243544827 rs11583636 1.02E-09 phen CTSS 1 46656964 UQCRH 1:243544827 rs11584024 2.92E-08 phen UQCRH 1 205034723 NUAK2 1:243544827 rs11588412 7.76E-06 phen NUAK2 1 78575849 USP33 1:243544827 rs11589864 0.000213276803807025 phen USP33 1 207955963 IL20 1:243544827 rs115906510 2.85E-05 phen IL20 10 27821004 RAB18 1:243544827 rs11598492 0.000266826167729231 phen RAB18 11 196944 BET1L 1:243544827 rs11604127 3.66E-06 phen BET1L 11 47725306 MYBPC3 1:243544827 rs11604825 5.44E-09 phen MYBPC3 11 75055107 ARRB1 1:243544827 rs11604864 8.58E-05 phen ARRB1 11 129718478 NFRKB 1:243544827 rs11607337 0.000272910886026419 phen NFRKB 11 62210081 B3GAT3 1:243544827 rs11607566 0.000197821988179421 phen B3GAT3 6 32638146 GPSM3 1:243544827 rs116081545 0.000160755177393362 phen GPSM3 12 29920088 TMTC1 1:243544827 rs11609828 1.74E-14 phen TMTC1 12 125494940 BRI3BP 1:243544827 rs11614174 9.08E-05 phen BRI3BP 12 33019436 C12orf35 1:243544827 rs11615313 2.51E-05 phen C12orf35 9 132613008 FNBP1 1:243544827 rs116214654 6.11E-07 phen FNBP1 14 76470655 C14orf118 1:243544827 rs11623313 0.000164176117100563 phen C14orf118 4 76826582 NAAA 1:243544827 rs116248809 4.86E-16 phen NAAA 14 21347911 RNASE2 1:243544827 rs11626267 4.14E-05 phen RNASE2 14 90968808 CCDC88C 1:243544827 rs11628344 0.000137822895800724 phen CCDC88C 14 24844054 GMPR2 1:243544827 rs11628929 0.000177690090615231 phen GMPR2 15 76608686 ETFA 1:243544827 rs11631423 2.45E-07 phen ETFA 6 31678028 LY6G5C 1:243544827 rs116336999 1.12E-13 phen LY6G5C 6 26208269 ??? 1:243544827 rs116337444 5.43E-27 phen ??? 6 31445771 MICB 1:243544827 rs116345750 2.41E-16 phen MICB 15 75088962 CSK 1:243544827 rs11635664 1.10E-09 phen CSK 15 90882643 IDH2 1:243544827 rs11638227 0.000178232994194828 phen IDH2

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[turner]

Hi Selim,

I have been unable to reproduce thus bug. Can you send me your test file?

Thanks, Doug

[turner]

send to douglass.turner@gmail.com

[jrobinso]

@turner Sample data is above, in this thread.

[turner]

Hi Selim, I found the bug. The fix is on the way. -Doug

[selimkal]

Awesome! Looking forward to it!

Thanks!

Selim

On Wed, Apr 19, 2017 at 8:57 AM, Douglass Turner notifications@github.com wrote:

Hi Selim, I found the bug. The fix is on the way. -Doug

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[jrobinso]

Should be fixed now

[selimkal]

I am sorry, but I am still not getting any popup windows...

To remind you, I am using "https://igv.org/web/beta/igv-beta.js" version of IGV embedded in my webpage. So, maybe it was not fixed in that version?

Best, Selim

On Wed, Apr 19, 2017 at 11:14 AM, Jim Robinson notifications@github.com wrote:

Closed #385 https://github.com/igvteam/igv/issues/385.

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[jrobinso]

Its fixed in the git repository, the beta build is updated nightly.

On Wed, Apr 19, 2017 at 9:52 AM selimkal notifications@github.com wrote:

I am sorry, but I am still not getting any popup windows...

To remind you, I am using "https://igv.org/web/beta/igv-beta.js" version of IGV embedded in my webpage. So, maybe it was not fixed in that version?

Best, Selim

On Wed, Apr 19, 2017 at 11:14 AM, Jim Robinson notifications@github.com wrote:

Closed #385 https://github.com/igvteam/igv/issues/385.

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[selimkal]

Great job! Thanks a lot!

Selim

On Wed, Apr 19, 2017 at 1:00 PM, Jim Robinson notifications@github.com wrote:

Its fixed in the git repository, the beta build is updated nightly.

On Wed, Apr 19, 2017 at 9:52 AM selimkal notifications@github.com wrote:

I am sorry, but I am still not getting any popup windows...

To remind you, I am using "https://igv.org/web/beta/igv-beta.js" version of IGV embedded in my webpage. So, maybe it was not fixed in that version?

Best, Selim

On Wed, Apr 19, 2017 at 11:14 AM, Jim Robinson <notifications@github.com

wrote:

Closed #385 https://github.com/igvteam/igv/issues/385.

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