Variant report

Variant	rs656565
Chromosome Location	chr11:56300884-56300885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10400288	0.94[ASN][1000 genomes]
rs10501354	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs10736676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10736677	0.82[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.97[ASN][1000 genomes]
rs10736678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs10750820	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10792038	0.82[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap]
rs10792039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10792040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[ASN][1000 genomes]
rs10896480	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11228212	0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs11228641	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11228673	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11228676	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap]
rs11228684	0.88[ASN][1000 genomes]
rs11228686	0.88[ASN][1000 genomes]
rs11228687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11228693	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11228694	0.82[ASN][1000 genomes]
rs11228698	0.82[ASN][1000 genomes]
rs11228701	0.82[ASN][1000 genomes]
rs11228706	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11228708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11228710	0.82[ASW][hapmap]
rs11228715	0.84[LWK][hapmap]
rs12222989	0.82[ASN][1000 genomes]
rs12223492	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12418150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12418301	0.88[ASN][1000 genomes]
rs1397050	0.84[MKK][hapmap]
rs1473592	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1605924	0.88[ASN][1000 genomes]
rs17150739	1.00[ASN][1000 genomes]
rs1945196	1.00[ASN][1000 genomes]
rs1945206	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1945210	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1945261	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1945263	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1945282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs2202932	0.88[ASN][1000 genomes]
rs2511143	0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2865516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs33995115	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3938998	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4500505	1.00[ASN][1000 genomes]
rs4939034	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4939035	0.88[ASN][1000 genomes]
rs4939043	0.94[ASN][1000 genomes]
rs4939061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4939065	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4939066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs583216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs583589	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588805	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs592744	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs596212	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs597680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs600187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs611397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs614942	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61710550	0.82[ASN][1000 genomes]
rs628524	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs637912	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642630	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643384	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645351	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs646286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs654634	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655779	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6591323	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs6591381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs674431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs676901	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688832	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap]
rs7924528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7928704	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs7939886	1.00[ASN][1000 genomes]
rs971758	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050024	chr11:55900482-56518943	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
2	nsv497854	chr11:55917298-56537994	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv971949	chr11:56126625-56344170	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
4	nsv1046487	chr11:56228761-56310644	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv468576	chr11:56299930-56420029	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv555099	chr11:56299930-56420029	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs656565	APLNR	cis	parietal	SCAN
rs656565	MS4A3	cis	parietal	SCAN
rs656565	OR8J1	cis	cerebellum	SCAN
rs656565	OR5B2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56298400-56302000	Enhancers	Fetal Intestine Large	intestine
2	chr11:56299400-56301200	Enhancers	Fetal Intestine Small	intestine
3	chr11:56299800-56301000	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links