Variant report

Variant	rs17092220
Chromosome Location	chr10:116412194-116412195
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	chr10:116406490..116408753-chr10:116411218..116414182,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10885587	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10885588	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10885591	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10885593	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10885596	1.00[AFR][1000 genomes]
rs11196805	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11196811	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11196812	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11196815	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11196817	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11196818	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11196820	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11196829	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11196831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11196839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11196846	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11196865	1.00[AFR][1000 genomes]
rs12161653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12219039	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12571734	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12572646	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12573191	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17092202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2497668	0.84[EUR][1000 genomes]
rs2497681	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2497682	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4447090	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][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

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116394400-116422600	Weak transcription	Fetal Intestine Small	intestine
2	chr10:116399800-116413800	Weak transcription	Spleen	Spleen
3	chr10:116403200-116412200	Weak transcription	Brain Anterior Caudate	brain
4	chr10:116404800-116412200	Weak transcription	Lung	lung
5	chr10:116405200-116413400	Weak transcription	Colonic Mucosa	Colon
6	chr10:116406200-116412800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:116406200-116422000	Weak transcription	Fetal Lung	lung
8	chr10:116408200-116412800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr10:116408400-116415600	Enhancers	HUVEC	blood vessel
10	chr10:116408600-116413600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:116408600-116422000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr10:116408600-116441400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr10:116408800-116413000	Weak transcription	Psoas Muscle	Psoas
14	chr10:116408800-116427400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr10:116409000-116414600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:116409400-116414200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:116409600-116413400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:116409600-116414200	Weak transcription	NHEK	skin
19	chr10:116409600-116414400	Weak transcription	Placenta	Placenta
20	chr10:116409600-116414400	Weak transcription	Hela-S3	cervix
21	chr10:116409600-116421200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:116409600-116423600	Weak transcription	Esophagus	oesophagus
23	chr10:116410200-116412800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr10:116410200-116414400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:116410200-116414600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:116410200-116414800	Weak transcription	HSMMtube	muscle
27	chr10:116410400-116414400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:116410800-116412200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr10:116410800-116412400	Weak transcription	Stomach Mucosa	stomach
30	chr10:116410800-116413800	Enhancers	Liver	Liver
31	chr10:116410800-116422000	Weak transcription	Brain Hippocampus Middle	brain
32	chr10:116411000-116412200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr10:116411000-116412200	Weak transcription	Ovary	ovary
34	chr10:116411000-116412600	Weak transcription	A549	lung
35	chr10:116411000-116415800	Enhancers	Right Ventricle	heart
36	chr10:116411000-116417400	Enhancers	Right Atrium	heart
37	chr10:116411200-116412200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr10:116411200-116412800	Weak transcription	Gastric	stomach
39	chr10:116411200-116413600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr10:116411400-116414400	Weak transcription	HepG2	liver
41	chr10:116411400-116415800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr10:116411400-116418800	Enhancers	Fetal Heart	heart
43	chr10:116411600-116415200	Enhancers	Adipose Nuclei	Adipose
44	chr10:116411800-116412800	Weak transcription	Left Ventricle	heart
45	chr10:116411800-116412800	Weak transcription	Pancreas	Pancrea
46	chr10:116412000-116412200	Enhancers	Brain Inferior Temporal Lobe	brain

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