Variant report

Variant	rs12092948
Chromosome Location	chr1:197689967-197689968
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	chr1:197688429..197690737-chr1:197693121..197696010,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10737693	0.93[ASN][1000 genomes]
rs11583319	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11588864	1.00[ASN][1000 genomes]
rs11799915	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12117045	0.93[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[ASN][1000 genomes]
rs12131588	0.99[ASN][1000 genomes]
rs12141028	0.93[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs12354257	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421399	0.89[ASN][1000 genomes]
rs1539414	0.93[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs1573100	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16841842	0.96[ASN][1000 genomes]
rs16841904	0.93[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16841912	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17564924	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1775448	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1775452	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1998598	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2477059	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477073	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477077	0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs2488389	0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[ASN][1000 genomes]
rs2488391	0.88[ASN][1000 genomes]
rs2488393	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2488397	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2488398	0.92[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs2488401	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs2884629	0.88[ASN][1000 genomes]
rs35939830	0.88[ASN][1000 genomes]
rs4316387	0.87[ASN][1000 genomes]
rs6702421	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv873077	chr1:197615391-197698103	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv548873	chr1:197664905-197694037	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv3453738	chr1:197687700-197690857	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3453739	chr1:197687889-197690752	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197665800-197693600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:197688000-197692200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:197688000-197707400	Weak transcription	Left Ventricle	heart
4	chr1:197688600-197694200	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links