Table 2 Haplotype analysis for Ath30 on chromosome 1 and Ath22 on chromosome 15
Ath30 (50-90 Mb)High alleleLow allele
ChrPositionGenedbSNPB6DBA_2J129S1_SvImC3H_HeJCsqAmino acidAA coordinateSIFT
164690848Ccnyl1rs3682263CGG5_prime_utr_variant
164737532Fzd5rs30864875AGG5_prime_utr_variant
165050833Crygers31896846G-AAmissense_variantT/I940
165051094Crygers30805491T-CCmissense_variantE/G70
178499361BC035947GAAmissense_variant
178499653BC035947GAAmissense_variant
178511226Mogat1AGGsplice_region_variant
178537971Mogat1CTTmissense_variantT/I2940.4
178665012Utp14bGAAmissense_variantR/Q2091
179435347Scg2rs8253473GTTmissense_variantP/Q5531
179761838Wdfy1rs51597504ACC5_prime_utr_variant
179776115Mrpl44rs50597413TCC5_prime_utr_variant
181269388Nyap2rs30198875AGGmissense_variant
185778602A630001G21Rikrs223873695CTT5_prime_utr_variant
186303891B3gnt7rs31395357CTT5_prime_utr_variant
186304255B3gnt7rs33048624AGGsplice_region_variant
186306217B3gnt7rs31277682AGGmissense_variantQ/R3950.09
Ath22 (1-30 Mb)Low alleleHigh alleleCsqAmino acidAA coordinateSIFT
ChrPositionGenedbSNPB6AKR_JC3H_HeJDBA_2J
15128180916030458C11Rikrs3681822CTTmissense_variant
15128182166030458C11Rikrs32031213CTTmissense_variant
15128214446030458C11Rikrs31704434AGGmissense_variant
15128245056030458C11Rikrs48279007TGGmissense_variant
1512824880Droshars38201751CGG5_prime_utr_variant
1512824925Droshars31833279CTT5_prime_utr_variant
1512833943Droshars13470543GAAmissense_variantQ44
1513041377Cdh6rs31868071T-CCmissense_variantS/G5340.03
15251489899230109A22Rikrs32435878AGG5_prime_utr_variant
1525413714Basp1rs237680064AGG5_prime_utr_variant
1525414436Gm5468rs108432668AGGmissense_variant
1527562809Ankrs31625299CTTmissense_variantA/V2010.37
1528269390Dnah5rs256383837TCCmissense_variantV/A8920.61
1528269407Dnah5rs32933300GTTmissense_variantA/S8980.79
1528270500Dnah5rs32933295CTTmissense_variantH/Y9831
1528345815Dnah5rs31986690C-TTmissense_variantR/W24340.04
  • Candidate genes with functional significance are denoted in bold. A low SIFT score hinting a high likelihood of changes in protein function is denoted in red. Chr, chromosome; dbSNP, Single Nucleotide Polymorphism Database identifier; SIFT, Sorting Intolerant From Tolerant; Csq, DNA sequence variation; UTR, untranslated region.