Variant report

Variant	rs11196865
Chromosome Location	chr10:116437174-116437175
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	chr10:116425468..116427951-chr10:116436410..116438514,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10885591	0.85[MKK][hapmap];1.00[AFR][1000 genomes]
rs10885592	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[AFR][1000 genomes]
rs10885593	1.00[AFR][1000 genomes]
rs10885596	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11196818	1.00[AFR][1000 genomes]
rs11196820	1.00[AFR][1000 genomes]
rs11196829	1.00[AFR][1000 genomes]
rs11196831	1.00[AFR][1000 genomes]
rs11196832	1.00[AFR][1000 genomes]
rs11196833	1.00[AFR][1000 genomes]
rs11196834	1.00[AFR][1000 genomes]
rs11196836	1.00[AFR][1000 genomes]
rs11196838	1.00[AFR][1000 genomes]
rs11196839	1.00[AFR][1000 genomes]
rs11196842	1.00[AFR][1000 genomes]
rs11196846	1.00[AFR][1000 genomes]
rs11196864	0.81[JPT][hapmap]
rs11196867	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11196873	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11196876	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11196877	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11196884	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11196905	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[MEX][hapmap]
rs12161653	1.00[AFR][1000 genomes]
rs12572646	1.00[AFR][1000 genomes]
rs12573191	1.00[AFR][1000 genomes]
rs17092202	1.00[AFR][1000 genomes]
rs17092207	1.00[AFR][1000 genomes]
rs17092213	1.00[AFR][1000 genomes]
rs17092218	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[AFR][1000 genomes]
rs17092220	1.00[AFR][1000 genomes]
rs4447090	1.00[AFR][1000 genomes]
rs951268	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11196865	PRDM8	trans	parietal	SCAN
rs11196865	TCF7L2	cis	parietal	SCAN
rs11196865	KIAA1598	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116408600-116441400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr10:116415600-116438200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:116424200-116443000	Weak transcription	Esophagus	oesophagus
4	chr10:116425400-116441400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr10:116425800-116438200	Weak transcription	Adipose Nuclei	Adipose
6	chr10:116426400-116437600	Weak transcription	Fetal Heart	heart
7	chr10:116427600-116438600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:116429800-116438600	Weak transcription	Brain Anterior Caudate	brain
9	chr10:116431600-116444000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:116432400-116441600	Weak transcription	Fetal Intestine Small	intestine
11	chr10:116433800-116440200	Weak transcription	Lung	lung
12	chr10:116434000-116440200	Weak transcription	Right Atrium	heart
13	chr10:116434200-116441600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr10:116435000-116444000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr10:116435600-116441400	Weak transcription	Fetal Intestine Large	intestine
16	chr10:116436600-116437400	Enhancers	Left Ventricle	heart
17	chr10:116436800-116437200	Weak transcription	Right Ventricle	heart
18	chr10:116437000-116437600	Enhancers	Brain Hippocampus Middle	brain

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