Variant report

Variant	rs9989778
Chromosome Location	chr2:173583779-173583780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173578673..173581194-chr2:173583046..173585824,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10178654	1.00[JPT][hapmap]
rs10180021	1.00[JPT][hapmap]
rs10188540	0.85[ASN][1000 genomes]
rs10198425	0.85[ASN][1000 genomes]
rs10198426	0.85[ASN][1000 genomes]
rs10198546	0.85[ASN][1000 genomes]
rs10199472	1.00[JPT][hapmap]
rs10201129	1.00[JPT][hapmap]
rs10202550	1.00[JPT][hapmap]
rs10208151	1.00[JPT][hapmap]
rs10210546	1.00[JPT][hapmap]
rs11887454	1.00[JPT][hapmap]
rs11890159	1.00[JPT][hapmap]
rs11897396	0.85[ASN][1000 genomes]
rs11898565	1.00[JPT][hapmap]
rs11902043	0.85[ASN][1000 genomes]
rs11904366	1.00[JPT][hapmap]
rs12328591	0.85[ASN][1000 genomes]
rs12328781	0.85[ASN][1000 genomes]
rs12329241	0.85[ASN][1000 genomes]
rs12693005	1.00[JPT][hapmap]
rs13007707	1.00[JPT][hapmap]
rs13385403	1.00[JPT][hapmap]
rs13385676	0.85[ASN][1000 genomes]
rs13392808	1.00[JPT][hapmap]
rs13394924	1.00[JPT][hapmap]
rs13400719	0.85[ASN][1000 genomes]
rs13408965	0.85[ASN][1000 genomes]
rs13410779	1.00[CHD][hapmap]
rs13411408	0.85[ASN][1000 genomes]
rs13415156	1.00[JPT][hapmap]
rs13417334	1.00[JPT][hapmap]
rs13417913	0.85[ASN][1000 genomes]
rs13423248	0.85[ASN][1000 genomes]
rs16860696	1.00[JPT][hapmap]
rs16860697	1.00[JPT][hapmap]
rs17299956	1.00[JPT][hapmap]
rs17702263	1.00[JPT][hapmap]
rs1869922	1.00[JPT][hapmap]
rs2167374	0.85[ASN][1000 genomes]
rs28541707	0.85[ASN][1000 genomes]
rs28690076	0.85[ASN][1000 genomes]
rs3816536	1.00[JPT][hapmap]
rs62168072	0.85[ASN][1000 genomes]
rs62168078	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723872	1.00[JPT][hapmap]
rs6724116	0.85[ASN][1000 genomes]
rs6752257	1.00[JPT][hapmap]
rs72893026	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9989778	CIR1	cis	cerebellum	SCAN
rs9989778	RAPGEF4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173582600-173590800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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