Gene,SNP,TaqMan Assay ID,VIC,FAM,Polymorphism,Type,Location,Context sequence,NCBI dbSNP ,Ancestral allele,NCBI dbSNP sequence,NCBI refSNP direction,Assay strand vs dbSNP,Total sample,Cases,Controls,"VIC/VIC, cases","VIC/FAM, cases","FAM/FAM, cases","VIC/VIC, controls","VIC/FAM, controls","FAM/FAM, controls","FAM, cases","FAM, controls","FAM, GIH HapMap",,Ref. for analysis,Ref. allele (dbSNP),Risk allele (dbSNP),"Risk allele freq, cases","Risk allele freq, controls"
,,,,,,,,,,,,,,n,n,n,n ,n ,n ,n ,n ,n ,%,%,%,,,,,,
AS3MT,rs10748835,C___2852804_10,A,G,"A/G, transition substitution",Missense mutation,Chr.10: 102900499 - 102900499 on Build GRCh38,AATTGTAAAATTTTATCTCTGTTCT[A/G]TGTAAGTCAACCTAAATCAAACAGA,A/G,A,AATTGTAAAATTTTATCTCTGTTCT[A/G]TGTAAGTCAACCTAAATCAAACAGA,Forward,Same,1283,666,617,154,312,200,134,297,186,0.53,0.54,0.49,,VIC,A,G,0.53,0.542139384
AS3MT,rs3740393,C__25804287_10,G,C,"G/C, transversion substitution",Intron,Chr.10:102876898 on Build GRCh38,GTTCCCCTATTCCTTTCTTTGTTAT[G/C]TGGGGTCAATGTAATCATTAATCAT,C/G/T,C,GTTCCCCTATTCCTTTCTTTGTTAT[C/G/T]TGGGGTCAATGTAATCATTAATCAT,Forward,Same,1320,690,630,432,232,26,391,215,24,0.21,0.21,0.29,,VIC,G,C,0.21,0.208730159
BHMT,rs3733890,C__11646606_20,A,G,"A/G, transition substitution",Missense mutation,Chr.5:79126136 on Build GRCh38,ATGAAGGAGGGCTTGGAGGCTGCCC[A/G]ACTGAAAGCTCACCTGATGAGCCAG,A/G,G,ATGAAGGAGGGCTTGGAGGCTGCCC[A/G]ACTGAAAGCTCACCTGATGAGCCAG,Forward,Same,1312,688,624,47,288,353,53,254,317,0.72,0.71,0.74,,FAM,G,A,0.28,0.288461538
FOLR1,rs1540087,C___8892983_10,A,G,"A/G, transition substitution",Intron,Chr.11:72190447 on Build GRCh38,CTTCTTACATTTAATCCTTGCAGGA[A/G]AAAGCTAAGCCTCAAGATAGTTTGC,C/T,C,GCAAACTATCTTGAGGCTTAGCTTT[C/T]TCCTGCAAGGATTAAATGTAAGAAG,Reverse,Opposite,1309,684,625,1,92,591,8,89,528,0.93,0.92,0.93,,FAM,C,T,0.07,0.084
FOLR1,rs2071010,C__15861044_10,A,G,"A/G, transition substitution",Intron,Chr.11:72189920 on Build GRCh38,CAGACCAGAGTGTGGCCTGCTCAAG[A/G]TTAAACGACAAGTTAGTGTTCATCC,A/G,G,CAGACCAGAGTGTGGCCTGCTCAAG[A/G]TTAAACGACAAGTTAGTGTTCATCC,Forward,Same,1321,690,631,22,177,491,17,152,462,0.84,0.85,0.8,,FAM,G,A,0.16,0.147385103
FOLR1,rs7109250,C__29370656_10,C,T,"C/T, transition substitution",Intron/UTR 5,Chr.11:72190626 on Build GRCh38,TATTCCCTGAGAGTACAGATTTCTC[C/T]GGCGTGGCCCTCAAGGTTAGTGAGT,C/T,T,TATTCCCTGAGAGTACAGATTTCTC[C/T]GGCGTGGCCCTCAAGGTTAGTGAGT,Forward,Same,1317,688,629,594,93,1,529,91,9,0.07,0.09,0.07,,VIC,C,T,0.07,0.086645469
FOLR2,rs2298444,C___3246777_1_,C,T,"C/T, transition substitution",Intron,Chr.11:72221370 on Build GRCh38,AGATTGAGGTAGGGTTTGGAAAATC[C/T]TCAAGGATTTGGGGTGGGGTGAAGA,A/G,G,TCTTCACCCCACCCCAAATCCTTGA[A/G]GATTTTCCAAACCCTACCTCAATCT,Reverse,Opposite,1323,692,631,116,322,254,96,309,226,0.6,0.6,0.56,,FAM,A,G,0.4,0.396988906
FOLR2,rs514933,C___1061079_20,C,T,"C/T, transition substitution",Intron,Chr.11:72219163 on Build GRCh38,TGGGTTAGGCTCCTCCTTTGGTGGG[C/T]GACAGACTAGGGAGTCGCTGGCTTT,A/G,G,AAAGCCAGCGACTCCCTAGTCTGTC[A/G]CCCACCAAAGGAGGAGCCTAACCCA,Reverse,Opposite,1289,674,615,108,300,266,105,292,218,0.62,0.59,0.63,,VIC,G,A,0.62,0.591869919
FOLR2,rs651646,C___1061081_10,A,T,"A/T, transversion substitution",Intron,Chr.11:72218482 on Build GRCh38,TCTGACCTCATTTGCCACCGTAGGG[A/T]TGGGGAGACTGAGGCAGGAGGTGAA,A/T,A,TCTGACCTCATTTGCCACCGTAGGG[A/T]TGGGGAGACTGAGGCAGGAGGTGAA,Forward,Same,1318,691,627,208,333,150,199,295,133,0.46,0.45,--,,VIC,A,T,0.46,0.447368421
FOLR2,rs651933,C___2139473_10,A,G,"A/G, transition substitution",--,Chr.11:72215616 on Build GRCh38,AGACAAATATTGCATGATTCCACTT[A/G]GACAAGGAACTTACAGTACAGTAGC,A/G,A,AGACAAATATTGCATGATTCCACTT[A/G]GACAAGGAACTTACAGTACAGTAGC,Forward,Same,1291,674,617,215,317,142,202,287,128,0.45,0.44,0.39,,VIC,A,G,0.45,0.440032415
MTHFD1,rs11627387,C___8665894_10,A,G,"A/G, transition substitution",Intron,Chr.14: 64457259 - 64457259 on Build GRCh38,TGAACGAAACAAAATTTAAAAGCAG[A/G]CAAGCCCTGTACCTCCTTTTGGTCT,A/G,A,TGAACGAAACAAAATTTAAAAGCAG[A/G]CAAGCCCTGTACCTCCTTTTGGTCT,Forward,Same,1300,679,621,55,273,351,43,238,340,0.72,0.74,0.7,,FAM,G,A,0.28,0.260869565
MTHFD1,rs1950902,C__11660791_1_,A,G,"A/G, transition substitution",Missense mutation,Chr.14:64415662 on Build GRCh38,AGATTGACTAGCATCAATGCTGGGA[A/G]ACTTGCTAGAGGTGACCTCAATGAC,C/T,T,GTCATTGAGGTCACCTCTAGCAAGT[C/T]TCCCAGCATTGATGCTAGTCAATCT,Reverse,Opposite,1326,693,633,13,150,530,9,111,513,0.87,0.9,0.94,,FAM,C,T,0.13,0.101895735
MTHFD1,rs2236224,C___1376138_1_,A,G,"A/G, transition substitution",Intron,Chr.14:64442433 on Build GRCh38,TGGTGGGTTGAAGTATCTGATTATC[A/G]GCAGTGTGCTGACGGCCAAAAGGAA,C/T,C,TTCCTTTTGGCCGTCAGCACACTGC[C/T]GATAATCAGATACTTCAACCCACCA,Reverse,Opposite,1290,674,616,107,327,240,104,298,214,0.6,0.59,0.66,,FAM,C,T,0.4,0.410714286
MTHFD1,rs2236225,C___1376137_10,A,G,"A/G, transition substitution",Missense mutation,Chr.14:64442127 on Build GRCh38,GGCAATTCCTCCATCATTGCAGACC[A/G]GATCGCACTCAAGCTTGTTGGCCCA,C/T,C,TGGGCCAACAAGCTTGAGTGCGATC[C/T]GGTCTGCAATGATGGAGGAATTGCC,Reverse,Opposite,1315,685,630,143,326,216,145,310,175,0.55,0.52,0.52,,FAM,C,T,0.45,0.476190476
MTHFR,rs1476413,C___8861304_10,C,T,"C/T, transition substitution",Intron,Chr.1:11792243 on Build GRCh38,GCTGGGTGTTTGCTCAACGAAGGGC[C/T]TGGTACTCTGTGGGAACCCTGGGGC,A/G,G,GCCCCAGGGTTCCCACAGAGTACCA[A/G]GCCCTTCGTTGAGCAAACACCCAGC,Reverse,Opposite,1321,690,631,229,323,138,221,291,119,0.43,0.42,0.44,,VIC,G,A,0.43,0.419175911
MTHFR,rs1801131,C____850486_20,G,T,"G/T, transversion substitution",Missense mutation,Chr.1:11794419 on Build GRCh38,AAGAACGAAGACTTCAAAGACACTT[G/T]CTTCACTGGTCAGCTCCTCCCCCCA,A/C,A,TGGGGGGAGGAGCTGACCAGTGAAG[A/C]AAGTGTCTTTGAAGTCTTCGTTCTT,Reverse,Opposite,1284,669,615,107,300,262,93,276,246,0.62,0.62,0.61,,FAM,A,C,0.38,0.375609756
MTHFR,rs1801133,C___1202883_20,G,A,"G/A, transition substitution",Missense mutation,Chr.1:11796321 on Build GRCh38,GAAAAGCTGCGTGATGATGAAATCG[G/A]CTCCCGCAGACACCTTCTCCTTCAA,C/T,C,TTGAAGGAGAAGGTGTCTGCGGGAG[C/T]CGATTTCATCATCACGCAGCTTTTC,Reverse,Opposite,1322,691,631,537,141,13,485,134,12,0.12,0.13,0.17,,VIC,C,T,0.12,0.125198098
MTR,rs1805087,C__12005959_10,A,G,"A/G, transition substitution",Missense mutation,Chr.1:236885200 on Build GRCh38,GAAGAATATGAAGATATTAGACAGG[A/G]CCATTATGAGTCTCTCAAGGTAAGT,A/G,A,GAAGAATATGAAGATATTAGACAGG[A/G]CCATTATGAGTCTCTCAAGGTAAGT,Forward,Same,1321,690,631,373,259,58,343,241,47,0.27,0.27,0.35,,VIC,A,G,0.27,0.265451664
MTRR,rs1801394,C___3068176_10,A,G,"A/G, transition substitution",Missense mutation,Chr.5:7870860 on Build GRCh38,AGGCAAAGGCCATCGCAGAAGAAAT[A/G]TGTGAGCAAGCTGTGGTACATGGAT,A/G,A,AGGCAAAGGCCATCGCAGAAGAAAT[A/G]TGTGAGCAAGCTGTGGTACATGGAT,Forward,Same,1317,686,631,181,320,185,143,292,196,0.5,0.54,--,,VIC,A,G,0.5,0.54199683
SHMT1,rs1979277,C___3063127_10,A,G,"A/G, transition substitution",Intron,Chr.17:18328782 on Build GRCh38,TCAGGCAGGCCAGGCAGAGGGAAGA[A/G]AGAGGCGAAGCTCTCAACCTCCTCC,A/G,G,TCAGGCAGGCCAGGCAGAGGGAAGA[A/G]AGAGGCGAAGCTCTCAACCTCCTCC,Forward,Same,1300,675,625,21,187,467,12,194,419,0.83,0.83,--,,FAM,G,A,0.17,0.1744
SLC19A1,rs1888530,C___1325122_20,C,T,"C/T, transition substitution",Intron,Chr.21:45516509 on Build GRCh38,GGGTGCCCATGAGGGCCAGAACGTC[C/T]CGCCTGGCAGAGCAGGGTGAGGAGA,C/T,T,GGGTGCCCATGAGGGCCAGAACGTC[C/T]CGCCTGGCAGAGCAGGGTGAGGAGA,Forward,Same,1312,688,624,172,328,188,160,302,162,0.51,0.5,0.56,,FAM,T,C,0.49,0.498397436
SLC46A1,rs1128162,C___2536574_10,A,C,"A/C, transversion substitution",UTR 3,Chr.17: 28394772 - 28394772 on Build GRCh38,ACCCAGTAAGCATTGACTCCAAAGG[A/C]ATGGGGTGAGCATTCCAAACTGGAG,G/T,T,CTCCAGTTTGGAATGCTCACCCCAT[G/T]CCTTTGGAGTCAATGCTTACTGGGT,Reverse,Opposite,1280,666,614,173,323,170,141,326,147,0.5,0.5,0.57,,VIC,T,G,0.5,0.504885993
TCN2,rs1801198,C____325467_10,C,G,"C/G, transversion substitution",--,Chr.22:30615623 on Build GRCh38,CAGTTCCTCATGACTTCCCCCATGC[C/G]TGGGGCAGAACTGGGAACAGCATGT,A/C/G,C,CAGTTCCTCATGACTTCCCCCATGC[A/C/G]TGGGGCAGAACTGGGAACAGCATGT,Forward,Same,1318,686,632,91,350,245,91,297,244,0.61,0.62,--,,FAM,G,C,0.39,0.378955696
TYMS,rs1001761,C___1637484_10,A,G,"A/G, transition substitution",Intron,Chr.18: 662103 - 662103 on Build GRCh38,CGGGGGGATCAACTGAGATGGCTTA[A/G]GATTTACCTGGATGCCTGCTCTGCT,C/T,C,AGCAGAGCAGGCATCCAGGTAAATC[C/T]TAAGCCATCTCAGTTGATCCCCCCG,Reverse,Opposite,1310,685,625,208,328,149,181,301,143,0.46,0.47,0.45,,FAM,C,T,0.54,0.5304
TYMS,rs2847149,C__26612435_10,A,G,"A/G, transition substitution",Intron,Chr.18:666371 on Build GRCh38,AGGTGGCGCTGCTGTGAAGCGCAGT[A/G]CCAGGGTCACACTCCACTCCCAGCT,A/G,G,AGGTGGCGCTGCTGTGAAGCGCAGT[A/G]CCAGGGTCACACTCCACTCCCAGCT,Forward,Same,1320,693,627,201,335,157,172,303,152,0.47,0.48,0.47,,FAM,G,A,0.53,0.515948963
TYMS,rs502396,C____786068_10,C,T,"C/T, transition substitution",Intron,Chr.18:659236 on Build GRCh38,ATTTAAAGATAAGTTTTTACACTTT[C/T]ATTTCTCTGTGGCTCGACACTTCTG,C/T,T,ATTTAAAGATAAGTTTTTACACTTT[C/T]ATTTCTCTGTGGCTCGACACTTCTG,Forward,Same,1318,689,629,214,323,152,196,285,148,0.46,0.46,0.36,,FAM,T,C,0.54,0.538155803