Variant report

Variant	rs11005901
Chromosome Location	chr10:52249387-52249388
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52248823..52250649-chr10:52255298..52257622,2	MCF-7	breast:
2	chr10:52229073..52233516-chr10:52246220..52249871,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225303	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10159614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10825837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs10825903	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11005454	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11005920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11815109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244472	1.00[AMR][1000 genomes]
rs12245522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246357	1.00[AMR][1000 genomes]
rs12251096	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12251514	0.93[EUR][1000 genomes]
rs12253726	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12253887	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12255967	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12265260	0.82[ASN][1000 genomes]
rs12265364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011770	0.82[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap]
rs61152656	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7077375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7097717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7097865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs73316672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73316673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73316690	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73332908	1.00[AMR][1000 genomes]
rs73332909	1.00[AMR][1000 genomes]
rs7358033	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916018	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52229800-52252000	Weak transcription	Aorta	Aorta
2	chr10:52230600-52256400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:52231200-52257800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr10:52234000-52261600	Weak transcription	Pancreas	Pancrea
5	chr10:52237000-52250400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:52237800-52255000	Weak transcription	Liver	Liver
7	chr10:52237800-52261800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:52243800-52250000	Weak transcription	Fetal Lung	lung
9	chr10:52244400-52261800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr10:52244800-52261800	Weak transcription	Primary T cells from cord blood	blood
11	chr10:52244800-52262000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr10:52246800-52251600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:52247000-52271200	Weak transcription	Colon Smooth Muscle	Colon
14	chr10:52247200-52255200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:52248000-52261800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr10:52248200-52256200	Weak transcription	Left Ventricle	heart
17	chr10:52248400-52249400	Enhancers	Brain Hippocampus Middle	brain
18	chr10:52248400-52250600	Enhancers	Fetal Heart	heart
19	chr10:52248600-52249400	Enhancers	Brain Anterior Caudate	brain
20	chr10:52248800-52249400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr10:52248800-52257600	Weak transcription	Ovary	ovary
22	chr10:52249200-52249400	Enhancers	HSMMtube	muscle
23	chr10:52249200-52266800	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links