Variant report

Variant	rs6466643
Chromosome Location	chr7:117739400-117739401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10247768	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10272234	0.88[EUR][1000 genomes]
rs11542074	0.82[EUR][1000 genomes]
rs11974039	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11983651	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12154684	0.84[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1544584	0.81[EUR][1000 genomes]
rs17140984	0.84[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs17141053	0.84[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap]
rs2215628	0.84[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2286863	0.82[EUR][1000 genomes]
rs2286865	0.84[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap]
rs2402300	0.93[ASN][1000 genomes]
rs33924981	0.82[EUR][1000 genomes]
rs34010516	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34019303	0.82[EUR][1000 genomes]
rs35218902	0.80[EUR][1000 genomes]
rs35485182	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs38828	0.88[EUR][1000 genomes]
rs45604739	0.82[EUR][1000 genomes]
rs4730837	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs62466471	0.81[EUR][1000 genomes]
rs62466515	0.82[EUR][1000 genomes]
rs62468297	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62469806	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6972105	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786233	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9641593	0.81[EUR][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	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1019337	chr7:117707746-117739400	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031419	chr7:117708734-117739400	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2752146	chr7:117739049-117792049	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1016264	chr7:117739146-117792988	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2761358	chr7:117739158-117793000	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv608260	chr7:117739400-117792838	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6466643	ANKRD7	cis	parietal	SCAN
rs6466643	KCND2	cis	parietal	SCAN
rs6466643	LSM8	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117738600-117739400	Enhancers	NHEK	skin
2	chr7:117738600-117739600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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