| 1 |
161476204 |
rs9427397 |
C |
T |
1892.35 |
PASS |
0.0807522123893805 |
NM_021642; NM_001136219 |
FCGR2A |
+ |
CDS |
. |
237;240 |
62;63 |
81;78 |
CAG |
Gln |
TAG |
Stop |
TRUE |
nonsense |
c.184C>T;c.187C>T |
p.Q62*;p.Q63* |
TRUE |
81;78 |
q23.3 |
ex3/7 |
. |
FCGR2A,Fc fragment of IgG, low affinity IIa, receptor (CD32),gene with protein product,CD32, CD32A, IGFR2, CDw32,Immunoglobulin G Fc receptor II,CD molecules,ENSG00000143226 |
. |
V$BRACH_01.chr1.161476185.161476209 |
. |
. |
TRUE |
TRUE |
. |
TRUE |
AC=2;AF=0.33;AN=6;BaseQRankSum=-4.326;DB;DP=179;Dels=0.00;FS=2.226;HRun=0;HaplotypeScore=3.7997;MQ=54.42;MQ0=0;MQRankSum=1.896;QD=16.46;ReadPosRankSum=-1.224;VQSLOD=4.1751;culprit=HaplotypeScore;DB;GMAF=0.0807522123893805;name=NM_021642;name2=FCGR2A;transcriptStrand=+;positionType=CDS;mrnaCoord=237;codonCoord=62;spliceDist=78;referenceCodon=CAG;referenceAA=Gln;variantCodon=TAG;variantAA=Stop;changesAA=true;functionalClass=nonsense;codingCoordStr=c.184C>T;proteinCoordStr=p.Q62*;inCodingRegion=true;name=NM_001136219;name2=FCGR2A;transcriptStrand=+;positionType=CDS;mrnaCoord=240;codonCoord=63;spliceDist=81;referenceCodon=CAG;referenceAA=Gln;variantCodon=TAG;variantAA=Stop;changesAA=true;functionalClass=nonsense;codingCoordStr=c.187C>T;proteinCoordStr=p.Q63*;inCodingRegion=true;name2=FCGR2A;name=NM_021642;transcriptStrand=+;exon=ex3/7;name2=FCGR2A;name=NM_001136219;transcriptStrand=+;exon=ex3/7;cytoBand=q23.3;HGNC_GeneAnnotation=FCGR2A,Fc fragment of IgG, low affinity IIa, receptor (CD32),gene with protein product,CD32, CD32A, IGFR2, CDw32,Immunoglobulin G Fc receptor II,CD molecules,ENSG00000143226;dgv_Cnv=True;abParts_IG_T_CelReceptors=True;conrad_Cnv=True;tfbsRegion=V$BRACH_01.chr1.161476185.161476209 |
| 1 |
161479745 |
. |
A |
G |
3424.25 |
PASS |
. |
NM_021642; NM_001136219 |
FCGR2A |
+ |
CDS |
1 |
550;553 |
166;167 |
-120 |
CAT |
His |
CGT |
Arg |
TRUE |
missense |
c.500A>G;c.497A>G |
p.H166R;p.H167R |
TRUE |
-120 |
q23.3 |
ex4/7 |
. |
FCGR2A,Fc fragment of IgG, low affinity IIa, receptor (CD32),gene with protein product,CD32, CD32A, IGFR2, CDw32,Immunoglobulin G Fc receptor II,CD molecules,ENSG00000143226 |
. |
. |
pubMedID=19915573 |
TRUE |
TRUE |
TRUE |
. |
TRUE |
AC=3;AF=0.50;AN=6;BaseQRankSum=-2.558;DB;DP=174;Dels=0.00;FS=15.149;HRun=0;HaplotypeScore=0.9431;MQ=57.65;MQ0=0;MQRankSum=0.474;QD=28.78;ReadPosRankSum=1.795;VQSLOD=4.9485;culprit=FS;name=NM_001136219;name2=FCGR2A;transcriptStrand=+;positionType=CDS;frame=1;mrnaCoord=553;codonCoord=167;spliceDist=-120;referenceCodon=CAT;referenceAA=His;variantCodon=CGT;variantAA=Arg;changesAA=true;functionalClass=missense;codingCoordStr=c.500A>G;proteinCoordStr=p.H167R;inCodingRegion=true;name=NM_021642;name2=FCGR2A;transcriptStrand=+;positionType=CDS;frame=1;mrnaCoord=550;codonCoord=166;spliceDist=-120;referenceCodon=CAT;referenceAA=His;variantCodon=CGT;variantAA=Arg;changesAA=true;functionalClass=missense;codingCoordStr=c.497A>G;proteinCoordStr=p.H166R;inCodingRegion=true;name2=FCGR2A;name=NM_021642;transcriptStrand=+;exon=ex4/7;name2=FCGR2A;name=NM_001136219;transcriptStrand=+;exon=ex4/7;cytoBand=q23.3;gwasCatalog=pubMedID=21297633,trait=Ulcerative colitis;gwasCatalog=pubMedID=19915573,trait=Ulcerative colitis;HGNC_GeneAnnotation=FCGR2A,Fc fragment of IgG, low affinity IIa, receptor (CD32),gene with protein product,CD32, CD32A, IGFR2, CDw32,Immunoglobulin G Fc receptor II,CD molecules,ENSG00000143226;dgv_Cnv=True;abParts_IG_T_CelReceptors=True;conrad_Cnv=True;genomicSuperDups=True;otherChrom=chr1;otherStart=161642750;otherEnd=161646894 |
| 1 |
144875979 |
rs71664005 |
G |
C |
7089.01 |
PASS |
0.161129568106312 |
NM_014644; NM_001198832; NM_001198834 |
PDE4DIP |
- |
CDS |
2 |
4992 |
1567 |
-3 |
CTC |
Leu |
CTG |
Leu |
FALSE |
silent |
c.4701C>G |
p.L1567L |
TRUE |
-3 |
q21.1 |
ex32/46;ex29/44 |
. |
PDE4DIP,phosphodiesterase 4D interacting protein,gene with protein product,KIAA0477, KIAA0454, MMGL,myomegalin,ENSG00000178104 |
. |
V$ARP1_01.chr1.144875978.144875994 |
. |
TRUE |
. |
TRUE |
. |
TRUE |
AC=2;AF=0.33;AN=6;BaseQRankSum=2.510;DB;DP=774;Dels=0.00;FS=1.803;HRun=0;HaplotypeScore=7.8851;MQ=59.29;MQ0=0;MQRankSum=-0.388;QD=13.53;ReadPosRankSum=1.023;VQSLOD=3.9036;culprit=HaplotypeScore;DB;GMAF=0.161129568106312;name=NM_014644;name2=PDE4DIP;transcriptStrand=-;positionType=CDS;frame=2;mrnaCoord=4992;codonCoord=1567;spliceDist=-3;referenceCodon=CTC;referenceAA=Leu;variantCodon=CTG;variantAA=Leu;changesAA=false;functionalClass=silent;codingCoordStr=c.4701C>G;proteinCoordStr=p.L1567L;inCodingRegion=true;spliceInfo=splice-donor_-3;name2=PDE4DIP;name=NM_001198834;transcriptStrand=-;exon=ex29/44;name2=PDE4DIP;name=NM_014644;transcriptStrand=-;exon=ex29/44;name2=PDE4DIP;name=NM_001198832;transcriptStrand=-;exon=ex32/46;cytoBand=q21.1;HGNC_GeneAnnotation=PDE4DIP,phosphodiesterase 4D interacting protein,gene with protein product,KIAA0477, KIAA0454, MMGL,myomegalin,ENSG00000178104;dgv_Cnv=True;conrad_Cnv=True;genomicSuperDups=True;otherChrom=chr1;otherStart=149035965;otherEnd=149106186;tfbsRegion=V$ARP1_01.chr1.144875978.144875994 |
| 1 |
19638309 |
rs2227295 |
A |
G |
81.96 |
PASS |
0.294912559618442 |
NM_003689; NM_001040125; NM_001040126; NM_017765 |
AKR7A2; PQLC2 |
+;- |
intron; putativePromoterRegion |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
FALSE |
. |
p36.13 |
. |
. |
AKR7A2,aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase),gene with protein product,AFAR,Aldo-keto reductases,ENSG00000053371 |
. |
. |
. |
. |
. |
. |
. |
. |
AC=1;AF=0.17;AN=6;BaseQRankSum=-0.937;DB;DP=34;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=6.4056;MQ=53.72;MQ0=0;MQRankSum=1.618;QD=5.46;ReadPosRankSum=-0.341;VQSLOD=3.8485;culprit=QD;DB;GMAF=0.294912559618442;name=NM_003689;name2=AKR7A2;transcriptStrand=-;positionType=intron;inCodingRegion=false;name2=PQLC2;name=NM_017765;transcriptStrand=+;putativePromoterRegion=CpG:129;name2=PQLC2;name=NM_001040126;transcriptStrand=+;putativePromoterRegion=CpG:129;name2=PQLC2;name=NM_001040125;transcriptStrand=+;putativePromoterRegion=CpG:129;cytoBand=p36.13;HGNC_GeneAnnotation=AKR7A2,aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase),gene with protein product,AFAR,Aldo-keto reductases,ENSG00000053371 |
| 1 |
179504034 |
. |
GAAGAAC |
G |
71 |
PASS |
. |
NM_144696 |
AXDND1 |
+ |
CDS |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
q25.2 |
ex25/26 |
. |
AXDND1,axonemal dynein light chain domain containing 1,gene with protein product,FLJ32940,ENSG00000162779 |
. |
. |
. |
. |
. |
. |
. |
. |
HP=2;NF=6;SF;NR=10;CA=0;DP=313;cytoBand=q25.2;name2=AXDND1;name=NM_144696;name2=AXDND1;name=NM_144696;transcriptStrand=+;positionType=CDS;exon=25/26;HGNC_GeneAnnotation=AXDND1,axonemal dynein light chain domain containing 1,gene with protein product,FLJ32940,ENSG00000162779 |
| 1 |
235353775 |
rs11409901 |
G |
GAA,GA |
100 |
PASS |
. |
NM_031371; NM_016374; NR_039908; NM_001206794 |
MIR4753; ARID4B |
- |
non_coding_intron, intron |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
q42.3 |
. |
CARDIOVASCULAR |
ARID4B,AT rich interactive domain 4B (RBP1-like),gene with protein product,BCAA, BRCAA1, SAP180,ENSG00000054267 |
. |
. |
. |
. |
. |
. |
. |
. |
HP=10;DB;NF=22;NR=22;CA=0;DP=295;DB;cytoBand=q42.3;name2=ARID4B;name=NM_001206794;name2=ARID4B;name=NM_016374;name2=ARID4B;name=NM_031371;name2=ARID4B;name=NM_016374;transcriptStrand=-;positionType:CDS;intron;name2=ARID4B;name=NM_031371;transcriptStrand=-;positionType:CDS;intron;name2=ARID4B;name=NM_001206794;transcriptStrand=-;positionType:CDS;intron;name2=MIR4753;name=NR_039908;transcriptStrand=-;positionType=non_coding_intron;gadAll=CARDIOVASCULAR;HGNC_GeneAnnotation=ARID4B,AT rich interactive domain 4B (RBP1-like),gene with protein product,BCAA, BRCAA1, SAP180,ENSG00000054267 |
| 1 |
33328409 |
. |
G |
GGA |
100 |
PASS |
. |
NM_001171941; NM_001171940; NM_153756 |
FNDC5 |
- |
utr3 |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
p35.1 |
. |
. |
FNDC5,fibronectin type III domain containing 5,gene with protein product,FRCP2,ENSG00000160097 |
FNDC5:miR-34a/34b-5p/34c/34c-5p/449/449abc/699,chr1_33328402_33328409 |
. |
. |
. |
. |
TRUE |
. |
. |
HP=2;NR=10;NF=6;CA=0;DP=315;cytoBand=p35.1;name2=FNDC5;name=NM_001171940;name2=FNDC5;name=NM_153756;name2=FNDC5;name=NM_001171941;name2=FNDC5;name=NM_001171940;transcriptStrand=-;utr3;name2=FNDC5;name=NM_153756;transcriptStrand=-;utr3;name2=FNDC5;name=NM_001171941;transcriptStrand=-;utr3;miRNAsites=FNDC5:miR-34a/34b-5p/34c/34c-5p/449/449abc/699,chr1_33328402_33328409;HGNC_GeneAnnotation=FNDC5,fibronectin type III domain containing 5,gene with protein product,FRCP2,ENSG00000160097;dgv_Cnv=True |
| 1 |
152185761 |
P2_M_061510_1_583 |
A |
|
. |
. |
. |
NM_001009931 |
HRNR |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
q21.3 |
ex3/3 |
. |
HRNR,hornerin,gene with protein product,S100a18, S100A16,ENSG00000197915 |
. |
. |
. |
TRUE, overlap=100.0%, otherChrom=chr1, otherStart=152188549, otherEnd=152191366 |
FALSE |
TRUE, overlap=100.0% |
FALSE |
TRUE, overlap=92.12% |
CIEND=-102,88;CIPOS=-96,74;IMPRECISE;SVLEN=-1369;SVTYPE=DEL;VALIDATED;NOVEL;VALMETHOD=CGH;SVMETHOD=RP;END=152187130;cytoBand=q21.3;name2=HRNR;name=NM_001009931;name=NM_001009931;exon=ex3/3;HGNC_GeneAnnotation=HRNR,hornerin,gene with protein product,S100a18, S100A16,ENSG00000197915;abParts_IG_T_CelReceptors=False;conrad_Cnv=True,overlap=92.12%;mcCarroll_Cnv=False;dgv_Cnv=True,overlap=100.0%;genomicSuperDups=True,overlap=100.0%,otherChrom=chr1,otherStart=152188549,otherEnd=152191366 |
| 1 |
152278805 |
P2_M_061510_1_628 |
G |
|
. |
. |
. |
NM_002016 |
FLG |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
. |
q21.3 |
ex3/3 |
. |
FLG,filaggrin,gene with protein product,ENSG00000143631 |
. |
. |
. |
TRUE, genomicSuperDups=True, overlap=94.56%, otherChrom=chr1, otherStart=152280691, otherEnd=152286484 |
FALSE |
TRUE, overlap=0.72% |
FALSE |
TRUE, overlap=100.0% |
CIEND=-102,88;CIPOS=-96,74;IMPRECISE;SVLEN=-1947;SVTYPE=DEL;VALIDATED;NOVEL;VALMETHOD=CGH;SVMETHOD=RP;END=152280752;cytoBand=q21.3;name2=FLG;name=NM_002016;name=NM_002016;exon=ex3/3;HGNC_GeneAnnotation=FLG,filaggrin,gene with protein product,ENSG00000143631;abParts_IG_T_CelReceptors=False;conrad_Cnv=True,overlap=100.0%;mcCarroll_Cnv=False;dgv_Cnv=True,overlap=0.72%;genomicSuperDups=True,overlap=94.56%,otherChrom=chr1,otherStart=152280691,otherEnd=152286484 |