Variant report

Variant	rs336564
Chromosome Location	chr3:161075149-161075150
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	chr3:64035675..64038032-chr3:161075125..161077341,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10513566	1.00[LWK][hapmap]
rs12488318	0.87[ASN][1000 genomes]
rs12494261	0.88[ASN][1000 genomes]
rs13318781	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs1450519	0.83[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1471440	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs1478567	0.88[ASN][1000 genomes]
rs163138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336544	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs336545	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs336546	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs336556	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs336565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336566	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs336571	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs336573	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336581	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336584	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419703	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4429651	0.81[ASN][1000 genomes]
rs4487256	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4490410	0.94[CHB][hapmap]
rs455739	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs458197	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs459067	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461616	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs462081	0.98[ASN][1000 genomes]
rs57201455	0.91[ASN][1000 genomes]
rs62278055	0.80[ASN][1000 genomes]
rs62279860	0.81[ASN][1000 genomes]
rs62279861	0.81[ASN][1000 genomes]
rs62279892	0.81[ASN][1000 genomes]
rs73160362	0.81[ASN][1000 genomes]
rs73162530	0.91[ASN][1000 genomes]
rs9290072	0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[AFR][1000 genomes]
rs9290075	0.87[ASN][1000 genomes]
rs978933	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs9811833	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs9812083	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs9825118	0.94[CHB][hapmap]
rs9827833	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs9828189	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs9828231	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs9836094	0.81[ASN][1000 genomes]
rs9839404	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs9857946	0.81[AFR][1000 genomes]
rs9859045	0.88[ASN][1000 genomes]
rs9876553	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs336564	ROCK1	trans	cerebellum	SCAN
rs336564	C3orf57	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:161064400-161083000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:161068200-161083200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:161068400-161075800	Weak transcription	Stomach Mucosa	stomach
5	chr3:161068400-161083200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:161068800-161079000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:161069600-161075400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:161070400-161075800	Weak transcription	Esophagus	oesophagus
9	chr3:161071600-161077000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:161073000-161075600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:161075000-161076200	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links