Variant report

Variant	rs10017712
Chromosome Location	chr4:86469434-86469435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10020489	0.82[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs10026535	0.83[ASN][1000 genomes]
rs10029852	0.89[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10032314	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1031988	0.83[MEX][hapmap]
rs11097059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11945598	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12501745	0.86[JPT][hapmap]
rs12506009	0.83[MEX][hapmap]
rs12506039	0.85[ASN][1000 genomes]
rs12506596	0.83[MEX][hapmap]
rs12510597	0.85[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12510645	0.80[ASN][1000 genomes]
rs12640411	0.83[MEX][hapmap]
rs12644974	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13139321	0.80[ASN][1000 genomes]
rs13140816	0.80[ASN][1000 genomes]
rs1384135	0.83[MEX][hapmap]
rs1545823	0.89[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17387199	0.82[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs17387344	0.82[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17389300	0.83[MEX][hapmap]
rs1994065	0.83[ASN][1000 genomes]
rs2062080	0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2128100	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2869352	0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34683578	0.83[ASN][1000 genomes]
rs4693702	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4693703	0.86[ASN][1000 genomes]
rs4693704	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4693716	0.83[MEX][hapmap]
rs58607125	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62315600	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6838692	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6839494	0.83[ASN][1000 genomes]
rs7657835	0.83[ASN][1000 genomes]
rs9994823	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10017712	TIGD2	cis	cerebellum	SCAN
rs10017712	AFF1	cis	parietal	SCAN
rs10017712	SNCA	cis	cerebellum	SCAN
rs10017712	ARHGAP24	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86454000-86476600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:86454600-86471800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:86454800-86471800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:86457800-86470400	Weak transcription	Primary B cells from cord blood	blood
5	chr4:86461000-86476600	Weak transcription	Left Ventricle	heart
6	chr4:86464600-86476400	Weak transcription	Gastric	stomach
7	chr4:86464800-86469600	Weak transcription	Fetal Heart	heart
8	chr4:86465000-86473000	Weak transcription	HSMM	muscle
9	chr4:86465400-86469600	Weak transcription	HSMMtube	muscle
10	chr4:86465400-86471000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:86466200-86469800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:86466800-86480600	Weak transcription	Esophagus	oesophagus
13	chr4:86469200-86470000	Enhancers	Primary B cells from peripheral blood	blood

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