Table 1 Strongest associated SNPs from the 52 genomic regions independently associated with eye color in the European discovery cohort (N = 157,485).

A full list of 115 independently associated SNPs from conditional analysis at these loci can be found in table ST1. SNPs with novel associations for eye color identified here are highlighted in bold. SNPs that were associated with other pigmentation traits, but not iris color, in previous studies are indicated by an asterisk (*). Chr is the chromosome for the given SNP, genome position (Pos) refer to the HG build 37, RS is the rsid for the given SNP, Freq is the allele frequency of the stated reference allele, Beta is the effect size for the stated reference allele, SE is the respective standard error for the beta, Alt allele is the alternative allele for the given SNP, and N is the sample size tested for the respective SNP.

RegionChrPosRSNearest geneRef alleleAlt alleleNFreqBetaSEP
119166344rs6693258GPR157TC1574830.216−0.0560.00919.86 × 10−10
2142110888rs6696511HIVEP3TC1574830.3820.1090.00771.35 × 10−45
31212421629rs351385*DTLGA1574830.580−0.0830.00752.31 × 10−28
41236035805rs2385028LYSTTC1574830.2450.0610.00862.43 × 10−12
5246233381rs13016869PRKCEGC1574830.208−0.0580.00922.23 × 10−10
62206950236rs112747614INO80DGC1574830.6960.0540.00813.69 × 10−11
72219755011rs121908120WNT10ATA1574830.9760.1400.02471.54 × 10−8
82223483670rs12614022FARSBGA1574830.6360.0480.00784.26 × 10−10
92239276278rs74409360TRAF3IP1TC1574830.076−0.1280.01408.09 × 10−20
10342762488rs3912104CCDC13TA1574830.5410.0450.00751.47 × 10−9
11369980177rs116359091*MITFGA1574830.974−0.2290.02461.02 × 10−20
12423939399rs4521336PPARGC1ATC1574830.3590.0480.00791.28 × 10−9
13459359559rs141318671No geneGA1574830.993−0.3180.05682.09 × 10−8
14490059434rs6828137TIGD2TG1574830.457−0.0410.00753.93 × 10−8
155311902rs62330021PDCD6, AHRRGA1574830.948−0.3250.01711.36 × 10−80
16533951693rs16891982*SLC45A2GC1574830.958−0.6540.01911.97 × 10−255
17540273518rs348613DAB2GA1574830.0010.7310.12272.54 × 10−9
185123896988rs72777200ZNF608TC1574830.8280.0740.01001.22 × 10−13
195148216187rs11957757ADRB2GA1574830.5470.0420.00752.94 × 10−8
206396321rs12203592*IRF4TC1574830.171−0.3850.01001.61 × 10−321
21610538183rs6910861GCNT2GA1574830.4610.0780.00761.20 × 10−24
226158841725rs341147TULP4GA1574830.343−0.0450.00786.45 × 10−9
23745960645rs2854746IGFBP3GC1574830.587−0.0430.00761.24 × 10−8
24783653553rs6944702SEMA3ATC1574830.5120.0480.00751.71 × 10−10
25812690997rs6997494LONRF1TG1574830.4800.0480.00741.07 × 10−10
26842003663rs12543326*AP3M2GA1574830.8750.0650.01139.07 × 10−9
27881350433rs147068120ZBTB10TC1574830.038−0.1220.01988.34 × 10−10
28912677471rs13297008*TYRP1GA1574830.3880.2600.00774.99 × 10−250
29927366436rs12552712MOB3BTC1574830.604−0.0560.00772.79 × 10−13
309132001056rs12335410IER5LTC1574830.221−0.0580.00901.28 × 10−10
311168831364rs72928978*TPCN2GA1574830.8770.1420.01216.42 × 10−32
321189017961rs1126809*TYRGA1574830.7210.2850.00831.82 × 10−255
331223979791rs9971729*SOX5CA1574830.5660.0820.00765.03 × 10−27
341292567833rs790464BTG1TC1574830.1890.0600.00964.50 × 10−10
351374178399rs2095645KLF12GA1574830.6720.0500.00793.26 × 10−10
361395189401rs9301973*DCTGA1574830.6710.0660.00801.48 × 10−16
371469236136rs138777265ZFP36L1CA1574830.047−0.1090.01766.21 × 10−10
381492780387rs17184180*SLC24A4TA1574830.5670.2710.00751.34 × 10−284
391528211758rs4778218*OCA2GA1574830.834−0.5200.0100<1 × 10−330
401528356859rs1129038*HERC2TC1574830.734−2.6050.0058<1 × 10−330
411548426484rs1426654SLC24A5GA1574830.1020.6840.06442.72 × 10−26
42161376386rs761063UBE2IGC1574830.277−0.0500.00842.07 × 10−9
43171966889rs4790309SMG6TC1574830.4560.0410.00753.71 × 10−8
441767497367rs3809761MAP2K6GA1574830.8110.0590.01015.08 × 10−9
451779612397rs6420484*TSPAN10GA1574830.645−0.1610.00807.53 × 10−90
46197581625rs73488486ZNF358TG1574830.0970.0860.01282.40 × 10−11
47204948248rs2748901SLC23A2GA1574830.463−0.0470.00753.37 × 10−10
482138568882rs2835660TTC3GC1574830.545−0.0640.00751.62 × 10−17
492144783287rs622330*SIK1GA1574830.5120.1110.00753.87 × 10−49
502246369657rs35051352WNT7BGC1478750.549−0.0620.00813.33 × 10−14
512348118832rs78542430SSX1TA1574830.450−0.0950.00625.93 × 10−53
5223119439335rs5957354TMEM255ATA1574830.861−0.0900.00925.43 × 10−23