Variant report

Variant	rs6546778
Chromosome Location	chr2:72819488-72819489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:72357423..72359989-chr2:72817889..72819964,2	MCF-7	breast:
2	chr2:72818726..72821056-chr2:72834950..72837136,2	MCF-7	breast:

Extended variants
information (count: 210 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:203)

rs_ID	r²[population]
rs10183056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10186080	1.00[ASN][1000 genomes]
rs10190674	1.00[ASN][1000 genomes]
rs10203965	1.00[ASN][1000 genomes]
rs10206555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10211019	1.00[ASN][1000 genomes]
rs1032982	1.00[CHB][hapmap]
rs10460572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496186	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865392	0.92[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126371	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126372	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126376	1.00[CHB][hapmap]
rs11126385	1.00[ASN][1000 genomes]
rs11676555	1.00[CHB][hapmap]
rs11677707	1.00[CHB][hapmap]
rs11679683	1.00[CHB][hapmap]
rs11684985	1.00[CHB][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685114	1.00[CHB][hapmap]
rs11686713	1.00[CHB][hapmap]
rs11894160	1.00[ASN][1000 genomes]
rs12052508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs12471136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471312	1.00[CHB][hapmap]
rs12476130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12618390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989141	1.00[ASN][1000 genomes]
rs12992973	1.00[CHB][hapmap]
rs12996319	1.00[CHB][hapmap]
rs12996406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12998681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006497	1.00[CHB][hapmap]
rs13008041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011477	1.00[CHB][hapmap]
rs13016873	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383535	1.00[ASN][1000 genomes]
rs13424607	1.00[ASN][1000 genomes]
rs1400580	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400581	1.00[CHB][hapmap]
rs1400582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1446887	1.00[CHB][hapmap]
rs1446888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446889	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446896	1.00[CHB][hapmap]
rs1508061	1.00[CHB][hapmap]
rs1517181	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1517185	1.00[CHB][hapmap]
rs1568145	1.00[ASN][1000 genomes]
rs1596930	1.00[CHB][hapmap]
rs1596931	1.00[CHB][hapmap]
rs1711838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503444	1.00[CHB][hapmap]
rs1911690	1.00[CHB][hapmap]
rs1992799	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2048171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2203679	1.00[CHB][hapmap]
rs2420565	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901146	1.00[CHB][hapmap]
rs3106879	1.00[ASN][1000 genomes]
rs3106880	1.00[ASN][1000 genomes]
rs3115351	1.00[CHB][hapmap]
rs34127669	1.00[ASN][1000 genomes]
rs4144318	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364045	1.00[CHB][hapmap]
rs4407272	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs4852293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852294	1.00[ASN][1000 genomes]
rs4852298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852873	1.00[CHB][hapmap]
rs4852874	1.00[CHB][hapmap]
rs4852875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852880	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852883	1.00[CHB][hapmap]
rs4852886	1.00[CHB][hapmap]
rs4852888	1.00[CHB][hapmap]
rs4852889	1.00[CHB][hapmap]
rs4852890	1.00[CHB][hapmap]
rs4852891	1.00[CHB][hapmap]
rs4852893	1.00[ASN][1000 genomes]
rs581976	1.00[ASN][1000 genomes]
rs583673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs585938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587431	1.00[ASN][1000 genomes]
rs587744	1.00[CHB][hapmap]
rs589547	1.00[CHB][hapmap]
rs590345	1.00[CHB][hapmap]
rs597799	1.00[ASN][1000 genomes]
rs598547	1.00[ASN][1000 genomes]
rs602465	1.00[ASN][1000 genomes]
rs603324	1.00[ASN][1000 genomes]
rs613880	1.00[ASN][1000 genomes]
rs614653	1.00[ASN][1000 genomes]
rs619343	1.00[ASN][1000 genomes]
rs62149282	1.00[ASN][1000 genomes]
rs623095	1.00[ASN][1000 genomes]
rs625434	1.00[ASN][1000 genomes]
rs628432	1.00[CHB][hapmap]
rs630241	1.00[CHB][hapmap]
rs631550	1.00[ASN][1000 genomes]
rs632670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs634476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs634574	1.00[ASN][1000 genomes]
rs634785	1.00[ASN][1000 genomes]
rs634929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs636319	1.00[ASN][1000 genomes]
rs636332	1.00[ASN][1000 genomes]
rs636734	1.00[ASN][1000 genomes]
rs640610	1.00[CHB][hapmap]
rs641123	1.00[ASN][1000 genomes]
rs642652	1.00[CHB][hapmap]
rs642847	1.00[ASN][1000 genomes]
rs645489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs646357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs647242	1.00[CHB][hapmap]
rs647269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs650352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs653220	1.00[CHB][hapmap]
rs653842	1.00[ASN][1000 genomes]
rs654157	1.00[ASN][1000 genomes]
rs6546765	1.00[ASN][1000 genomes]
rs6546776	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546781	1.00[CHB][hapmap]
rs6546782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs656440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs658067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs659833	1.00[CHB][hapmap]
rs661395	1.00[ASN][1000 genomes]
rs663218	1.00[CHB][hapmap]
rs664652	1.00[ASN][1000 genomes]
rs666361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs669074	1.00[ASN][1000 genomes]
rs6707435	1.00[ASN][1000 genomes]
rs6714580	1.00[ASN][1000 genomes]
rs6714595	1.00[CHB][hapmap]
rs671550	1.00[ASN][1000 genomes]
rs671721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6724529	1.00[CHB][hapmap]
rs6736305	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6739002	1.00[ASN][1000 genomes]
rs6741956	1.00[ASN][1000 genomes]
rs6742088	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6750766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758593	1.00[CHB][hapmap]
rs6761075	0.90[EUR][1000 genomes]
rs678684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs680380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs681574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs681908	1.00[ASN][1000 genomes]
rs683328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs684673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs687325	1.00[ASN][1000 genomes]
rs687371	1.00[ASN][1000 genomes]
rs688433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs689154	1.00[CHB][hapmap]
rs7420391	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420667	1.00[CHB][hapmap]
rs7560529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560599	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571064	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577238	1.00[CHB][hapmap]
rs7580268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7588400	1.00[CHB][hapmap]
rs7588602	1.00[ASN][1000 genomes]
rs7591025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592155	1.00[ASN][1000 genomes]
rs7598238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603797	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1008335	chr2:72561463-72819704	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv582208	chr2:72690622-72835886	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv834257	chr2:72701083-72853548	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6546778	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72809200-72833800	Weak transcription	Left Ventricle	heart
2	chr2:72817800-72821600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:72819400-72819600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:72819400-72819600	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links