Variant report

Variant	rs6953314
Chromosome Location	chr7:27116748-27116749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10257437	0.87[CEU][hapmap]
rs10257464	0.87[CEU][hapmap]
rs10259208	0.85[CEU][hapmap]
rs10276952	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11977871	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12673984	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12674308	0.90[ASN][1000 genomes]
rs12700771	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700785	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13230726	0.89[EUR][1000 genomes]
rs17427218	0.94[ASN][1000 genomes]
rs17436827	0.82[ASN][1000 genomes]
rs17437154	0.95[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs17448911	0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs17500459	0.86[AFR][1000 genomes]
rs213515	0.81[CEU][hapmap]
rs213516	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2140998	0.81[CEU][hapmap]
rs2259141	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2301719	1.00[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2693660	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2693661	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2693669	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712235	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs2712249	0.92[AFR][1000 genomes]
rs28357116	0.91[ASN][1000 genomes]
rs62454362	0.91[ASN][1000 genomes]
rs62454371	0.89[ASN][1000 genomes]
rs62454372	0.96[ASN][1000 genomes]
rs62454374	0.96[ASN][1000 genomes]
rs62454375	0.96[ASN][1000 genomes]
rs62457404	0.90[ASN][1000 genomes]
rs6948446	0.94[ASN][1000 genomes]
rs706015	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs774249	0.82[ASN][1000 genomes]
rs774250	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs774251	0.82[ASN][1000 genomes]
rs774252	0.87[CEU][hapmap]
rs774253	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs774256	0.80[ASN][1000 genomes]
rs774265	0.81[CEU][hapmap]
rs7791056	0.87[CEU][hapmap]
rs7797624	0.86[AFR][1000 genomes]
rs954051	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv887856	chr7:27073731-27297791	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6953314	HOXA10	cis	parietal	SCAN
rs6953314	DFNA5	cis	cerebellum	SCAN
rs6953314	STK31	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27105800-27118800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:27113200-27118400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links