Variant report

Variant	rs7562865
Chromosome Location	chr2:173382865-173382866
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	chr2:173378324..173380878-chr2:173382092..173384588,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10174809	0.83[ASW][hapmap];0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10178654	0.81[CEU][hapmap]
rs10180021	0.89[CEU][hapmap]
rs10199472	0.81[CEU][hapmap]
rs10201129	0.81[CEU][hapmap]
rs10202550	0.81[CEU][hapmap]
rs10208151	0.81[CEU][hapmap]
rs10210546	0.81[CEU][hapmap]
rs10451559	0.86[CEU][hapmap]
rs11886058	0.83[AFR][1000 genomes]
rs11887454	0.81[CEU][hapmap]
rs11890159	0.81[CEU][hapmap]
rs12052479	0.83[ASW][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap]
rs12465442	0.80[ASN][1000 genomes]
rs12693005	0.81[CEU][hapmap]
rs13007707	0.89[CEU][hapmap]
rs13012115	0.90[CEU][hapmap]
rs13021042	0.89[CEU][hapmap]
rs13033614	0.86[AFR][1000 genomes]
rs13385403	0.81[CEU][hapmap]
rs13392808	0.81[CEU][hapmap]
rs13394924	0.81[CEU][hapmap]
rs13398175	0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs13398305	0.90[CEU][hapmap]
rs13417334	0.81[CEU][hapmap]
rs1574257	0.86[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs16860543	0.86[CHB][hapmap]
rs16860696	0.81[CEU][hapmap]
rs16860697	0.81[CEU][hapmap]
rs17299956	0.81[CEU][hapmap]
rs17702263	0.81[CEU][hapmap]
rs17740327	0.90[CEU][hapmap]
rs1869922	0.81[CEU][hapmap]
rs34237921	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792259	0.90[CEU][hapmap]
rs4075604	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4972841	0.85[ASN][1000 genomes]
rs6723872	0.81[CEU][hapmap]
rs6752257	0.81[CEU][hapmap]
rs6755100	0.82[CHB][hapmap]
rs6759557	0.82[CHD][hapmap]
rs7560501	0.80[ASN][1000 genomes]
rs7562753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596665	0.90[CEU][hapmap]

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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7562865	LOC440925	cis	parietal	SCAN
rs7562865	ZAK	cis	cerebellum	SCAN
rs7562865	UBR3	cis	cerebellum	SCAN
rs7562865	G6PC2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173376400-173397400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:173377200-173386000	Weak transcription	Primary T cells from cord blood	blood
3	chr2:173378600-173383400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:173379800-173384200	Weak transcription	Primary B cells from cord blood	blood

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