Variant report

Variant	rs7694971
Chromosome Location	chr4:79629350-79629351
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79612403..79615054-chr4:79627599..79630387,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10008008	0.93[EUR][1000 genomes]
rs10008069	0.85[CHB][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs10029214	0.81[TSI][hapmap]
rs10084949	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1134123	0.82[EUR][1000 genomes]
rs1134124	0.82[EUR][1000 genomes]
rs11724233	0.80[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11931947	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13101941	0.82[AMR][1000 genomes]
rs13101964	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13114489	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13133277	0.94[EUR][1000 genomes]
rs1346144	0.97[EUR][1000 genomes]
rs1346145	0.91[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1469289	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469290	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1582759	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1806906	0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs1834519	0.81[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs1966537	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2867465	0.94[EUR][1000 genomes]
rs2867466	0.94[EUR][1000 genomes]
rs2903578	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4257676	0.88[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs4264856	0.87[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes]
rs4321658	0.91[EUR][1000 genomes]
rs4365753	0.87[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs4472162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4472163	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4495064	0.84[TSI][hapmap]
rs4560439	0.87[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4612	0.81[TSI][hapmap]
rs4619914	0.87[CEU][hapmap];0.84[CHB][hapmap];0.91[EUR][1000 genomes]
rs6533940	0.94[EUR][1000 genomes]
rs6533951	0.80[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs6818230	0.94[EUR][1000 genomes]
rs6825593	0.89[EUR][1000 genomes]
rs6842686	0.84[TSI][hapmap]
rs6842723	0.84[TSI][hapmap]
rs6855458	0.82[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs7672208	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677162	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699519	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699905	0.92[EUR][1000 genomes]
rs9992088	0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7694971	CXCL10	cis	parietal	SCAN
rs7694971	LIN54	cis	cerebellum	SCAN
rs7694971	ANXA3	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79625800-79629400	Enhancers	Brain Substantia Nigra	brain
2	chr4:79626000-79629400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr4:79626000-79629400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:79626000-79629400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr4:79626000-79629600	Enhancers	Primary B cells from peripheral blood	blood
6	chr4:79626000-79629600	Enhancers	Brain Hippocampus Middle	brain
7	chr4:79626200-79629400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr4:79626400-79631600	Weak transcription	HMEC	breast
9	chr4:79626600-79631600	Weak transcription	NHEK	skin
10	chr4:79628000-79629400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr4:79628200-79629400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr4:79628200-79629600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr4:79628400-79629400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:79628600-79629400	Flanking Active TSS	GM12878-XiMat	blood
15	chr4:79628800-79629400	Enhancers	Brain Cingulate Gyrus	brain
16	chr4:79628800-79629400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr4:79628800-79633000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:79629000-79629400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:79629000-79629400	Enhancers	Brain Angular Gyrus	brain
20	chr4:79629000-79629400	Enhancers	K562	blood
21	chr4:79629200-79629400	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links