Variant report

Variant	rs12510597
Chromosome Location	chr4:86478104-86478105
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10017712	0.85[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10020489	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10029756	0.82[ASN][1000 genomes]
rs10029852	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs10032314	0.92[ASN][1000 genomes]
rs11097059	0.82[CHD][hapmap]
rs11723931	0.88[ASN][1000 genomes]
rs11728289	0.88[ASN][1000 genomes]
rs11946933	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12108232	0.89[ASN][1000 genomes]
rs12500479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12501745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12506039	0.92[ASN][1000 genomes]
rs12510645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644974	0.92[ASN][1000 genomes]
rs13139321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545823	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs1548107	0.89[ASN][1000 genomes]
rs17387199	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs17387344	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1871824	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1871825	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994065	0.90[ASN][1000 genomes]
rs1994068	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs2062080	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2128092	0.89[ASN][1000 genomes]
rs2170418	0.88[ASN][1000 genomes]
rs2869352	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2869355	0.87[ASN][1000 genomes]
rs34662286	0.89[ASN][1000 genomes]
rs4693703	0.93[ASN][1000 genomes]
rs4693704	0.92[ASN][1000 genomes]
rs6838692	0.93[ASN][1000 genomes]
rs6839494	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7657835	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs964837	1.00[CHB][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.89[ASN][1000 genomes]
rs9760558	0.83[MEX][hapmap]
rs9994597	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9994823	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12510597	ARHGAP24	cis	lymphoblastoid	seeQTL
rs12510597	ARHGAP24	Cis_1M	lymphoblastoid	RTeQTL
rs12510597	TIGD2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86466800-86480600	Weak transcription	Esophagus	oesophagus
2	chr4:86475600-86488000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:86475800-86482400	Enhancers	Primary B cells from peripheral blood	blood
4	chr4:86476200-86478200	Enhancers	GM12878-XiMat	blood
5	chr4:86476400-86479400	Enhancers	Primary B cells from cord blood	blood
6	chr4:86476600-86479400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:86476800-86478200	Enhancers	Right Atrium	heart
8	chr4:86476800-86491800	Weak transcription	NHDF-Ad	bronchial
9	chr4:86477000-86493000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:86477200-86478600	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:86477200-86480400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:86477200-86487200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:86477400-86483800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:86477600-86486400	Weak transcription	HSMM	muscle
15	chr4:86477600-86494600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:86477800-86479000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:86478000-86478200	Enhancers	Pancreas	Pancrea
18	chr4:86478000-86479000	Enhancers	Spleen	Spleen
19	chr4:86478000-86479200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:86478000-86501000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links