Variant report

Variant	rs13153619
Chromosome Location	chr5:147723506-147723507
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10036053	0.92[EUR][1000 genomes]
rs10037318	0.91[EUR][1000 genomes]
rs10044054	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050560	0.84[CEU][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs10057472	0.94[EUR][1000 genomes]
rs10060180	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10060753	0.85[CEU][hapmap]
rs10068891	0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.97[MKK][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072817	0.90[EUR][1000 genomes]
rs10072958	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10077690	0.85[CEU][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs10476892	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477374	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515610	0.91[EUR][1000 genomes]
rs12516267	0.91[EUR][1000 genomes]
rs12519039	0.93[EUR][1000 genomes]
rs12521065	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12717971	0.99[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12717973	0.85[CEU][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs13157347	0.90[EUR][1000 genomes]
rs13158948	0.86[EUR][1000 genomes]
rs13176114	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13358385	0.93[EUR][1000 genomes]
rs1345741	0.82[CEU][hapmap];0.82[LWK][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1363704	0.92[EUR][1000 genomes]
rs1363705	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1363707	0.95[CEU][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1422968	0.99[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1422970	0.99[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1422976	0.95[CEU][hapmap]
rs1422977	0.86[EUR][1000 genomes]
rs1582519	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs17719578	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719662	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17719763	1.00[CEU][hapmap];0.92[YRI][hapmap];0.94[EUR][1000 genomes]
rs17719873	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17776554	0.93[EUR][1000 genomes]
rs17776674	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17776882	0.82[ASW][hapmap];0.81[LWK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs1862430	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862431	0.92[EUR][1000 genomes]
rs2161432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400509	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28442279	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2895761	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34001290	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34163281	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35006442	0.84[EUR][1000 genomes]
rs35700061	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs35792476	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749689	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs3749690	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4406123	0.86[EUR][1000 genomes]
rs4599524	0.86[LWK][hapmap]
rs4705247	0.82[CEU][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs4705248	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4705249	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs4705251	0.92[EUR][1000 genomes]
rs4705252	0.95[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs6580542	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580544	0.94[EUR][1000 genomes]
rs6580545	0.94[ASW][hapmap];0.95[CEU][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6580546	0.95[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6580548	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860261	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6865036	0.87[EUR][1000 genomes]
rs6865972	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866106	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875252	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875795	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6876308	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6876982	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6882932	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886203	0.92[EUR][1000 genomes]
rs6891724	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892647	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs6893378	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894032	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712350	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7713986	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716578	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722458	0.91[EUR][1000 genomes]
rs7729309	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7730707	0.94[EUR][1000 genomes]
rs7731526	0.93[EUR][1000 genomes]
rs7734458	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736728	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325094	0.91[EUR][1000 genomes]
rs9784645	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13153619	SPINK9	cis	parietal	SCAN
rs13153619	SPINK7	cis	uninvolved skin	skin_eQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147709400-147749200	Weak transcription	Psoas Muscle	Psoas
2	chr5:147713000-147728800	Weak transcription	Aorta	Aorta
3	chr5:147714800-147731200	Weak transcription	Pancreas	Pancrea
4	chr5:147721600-147723600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:147721600-147729000	Weak transcription	Left Ventricle	heart
6	chr5:147721800-147723800	Enhancers	HMEC	breast
7	chr5:147722400-147723600	Enhancers	Stomach Mucosa	stomach
8	chr5:147722600-147723800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:147722600-147723800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr5:147722600-147724200	Enhancers	K562	blood
11	chr5:147723200-147723600	Enhancers	Hela-S3	cervix
12	chr5:147723200-147726200	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links