Variant report

Variant	rs1856497
Chromosome Location	chr6:128581330-128581331
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	chr6:128581287..128583776-chr6:128604399..128606383,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10046162	0.82[EUR][1000 genomes]
rs10485161	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10485162	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499136	0.82[EUR][1000 genomes]
rs10499138	1.00[EUR][1000 genomes]
rs11961948	1.00[AMR][1000 genomes]
rs11962332	1.00[AMR][1000 genomes]
rs11962916	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11968433	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970637	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053270	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055290	1.00[EUR][1000 genomes]
rs17055300	1.00[EUR][1000 genomes]
rs17055360	1.00[EUR][1000 genomes]
rs17055365	1.00[EUR][1000 genomes]
rs17055403	1.00[EUR][1000 genomes]
rs17055412	1.00[EUR][1000 genomes]
rs17055415	1.00[EUR][1000 genomes]
rs17055421	1.00[EUR][1000 genomes]
rs17055443	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17055445	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17055461	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055488	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055499	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055501	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055507	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738273	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1768358	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28874136	0.82[EUR][1000 genomes]
rs4131020	1.00[EUR][1000 genomes]
rs4496822	0.82[EUR][1000 genomes]
rs4895832	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897244	1.00[EUR][1000 genomes]
rs4897245	1.00[EUR][1000 genomes]
rs4897246	1.00[EUR][1000 genomes]
rs4897247	1.00[EUR][1000 genomes]
rs4897248	1.00[EUR][1000 genomes]
rs4897249	1.00[EUR][1000 genomes]
rs4897250	1.00[EUR][1000 genomes]
rs55828045	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56042959	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56932458	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57797601	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58652879	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58706847	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59341107	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60264538	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60436012	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61111040	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61757810	1.00[AMR][1000 genomes]
rs6900798	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904846	1.00[AMR][1000 genomes]
rs6905735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909380	1.00[EUR][1000 genomes]
rs6910587	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913738	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6918772	1.00[EUR][1000 genomes]
rs6929394	1.00[EUR][1000 genomes]
rs6929623	1.00[EUR][1000 genomes]
rs6931593	1.00[AMR][1000 genomes]
rs6933133	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938199	1.00[EUR][1000 genomes]
rs73588698	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73590666	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73592613	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73592686	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746423	1.00[AMR][1000 genomes]
rs7751187	1.00[EUR][1000 genomes]
rs7752113	0.82[EUR][1000 genomes]
rs7754637	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768121	1.00[EUR][1000 genomes]
rs7772200	1.00[EUR][1000 genomes]
rs9491909	0.82[EUR][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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128551400-128584400	Weak transcription	Pancreas	Pancrea
2	chr6:128555200-128584400	Weak transcription	HMEC	breast
3	chr6:128555600-128595800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:128561400-128587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:128562800-128588200	Weak transcription	HUVEC	blood vessel
6	chr6:128563000-128585400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:128564400-128583400	Weak transcription	HepG2	liver
8	chr6:128564400-128588600	Weak transcription	NHEK	skin
9	chr6:128568000-128592000	Weak transcription	Brain Angular Gyrus	brain
10	chr6:128571200-128584200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:128571200-128596200	Weak transcription	HSMMtube	muscle
12	chr6:128574000-128588200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:128574000-128592200	Weak transcription	Gastric	stomach
14	chr6:128574000-128596200	Weak transcription	HSMM	muscle
15	chr6:128574400-128592600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:128574600-128596400	Weak transcription	NH-A	brain
17	chr6:128574800-128584800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:128574800-128587200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:128575000-128585000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:128576400-128584200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:128577400-128584000	Weak transcription	Fetal Intestine Small	intestine
22	chr6:128577600-128584200	Weak transcription	Liver	Liver
23	chr6:128577800-128584800	Weak transcription	Fetal Intestine Large	intestine
24	chr6:128579800-128581400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr6:128580000-128581400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:128580000-128581600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr6:128580000-128584000	Weak transcription	Left Ventricle	heart
28	chr6:128580000-128589000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:128580000-128592400	Weak transcription	Right Ventricle	heart
30	chr6:128580200-128581600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:128580400-128581600	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:128580400-128581600	Weak transcription	Psoas Muscle	Psoas
33	chr6:128580400-128592000	Weak transcription	Small Intestine	intestine
34	chr6:128580600-128581400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr6:128580600-128581600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:128580600-128581600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:128580600-128581800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:128580600-128581800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:128580600-128582000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:128580600-128583000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:128580600-128584800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:128580600-128587800	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:128580800-128581400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr6:128580800-128581400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:128580800-128582000	Active TSS	NHDF-Ad	bronchial
46	chr6:128581000-128581400	Active TSS	Osteobl	bone
47	chr6:128581000-128581800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:128581000-128582000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:128581000-128582000	Enhancers	Dnd41	blood
50	chr6:128581000-128582200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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