Variant report

Variant	rs56673339
Chromosome Location	chr2:86252183-86252184
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86053903..86054829-chr2:86251609..86252561,2	MCF-7	breast:
2	chr2:86252057..86252850-chr2:86306651..86307239,2	MCF-7	breast:
3	chr2:86128806..86129326-chr2:86252133..86252907,2	MCF-7	breast:
4	chr2:86114460..86116872-chr2:86251867..86254759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115525	Chromatin interaction
ENSG00000232504	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs2278086	0.96[AFR][1000 genomes]
rs2278537	1.00[AFR][1000 genomes]
rs34302587	0.93[AFR][1000 genomes]
rs35093541	0.96[AFR][1000 genomes]
rs36051710	0.96[AFR][1000 genomes]
rs3770086	1.00[AFR][1000 genomes]
rs3770091	1.00[AFR][1000 genomes]
rs57906735	1.00[AFR][1000 genomes]
rs58403969	1.00[AFR][1000 genomes]
rs58614836	0.89[AFR][1000 genomes]
rs59947468	0.90[AFR][1000 genomes]
rs60719866	0.96[AFR][1000 genomes]
rs60887312	0.83[AFR][1000 genomes]
rs61185790	1.00[AFR][1000 genomes]
rs6547656	1.00[AFR][1000 genomes]
rs6547657	1.00[AFR][1000 genomes]
rs6704777	1.00[AFR][1000 genomes]
rs6708146	1.00[AFR][1000 genomes]
rs6712535	1.00[AFR][1000 genomes]
rs6712576	1.00[AFR][1000 genomes]
rs6724612	0.93[AFR][1000 genomes]
rs6737211	1.00[AFR][1000 genomes]
rs6741815	1.00[AFR][1000 genomes]
rs6741832	1.00[AFR][1000 genomes]
rs6755224	1.00[AFR][1000 genomes]
rs6755246	0.96[AFR][1000 genomes]
rs7557349	1.00[AFR][1000 genomes]
rs7569577	1.00[AFR][1000 genomes]
rs7572206	1.00[AFR][1000 genomes]
rs7582484	1.00[AFR][1000 genomes]
rs7599656	1.00[AFR][1000 genomes]
rs7606062	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86244200-86257000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:86244400-86252400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:86244400-86252600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:86244400-86252800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:86244400-86253000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:86244400-86255000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:86244600-86252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:86244600-86252600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:86244600-86255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:86244600-86257200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:86244800-86253600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:86245000-86252400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:86245000-86252600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:86245400-86252400	Weak transcription	Esophagus	oesophagus
15	chr2:86245400-86252600	Weak transcription	Hela-S3	cervix
16	chr2:86245400-86254000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:86245400-86254600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:86245400-86257200	Weak transcription	Stomach Mucosa	stomach
19	chr2:86245400-86257400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:86245400-86263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:86245600-86252400	Weak transcription	NHEK	skin
22	chr2:86245600-86253600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:86246200-86252600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:86246200-86252600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr2:86246400-86252600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:86247400-86252600	Weak transcription	Fetal Brain Male	brain
27	chr2:86248000-86252400	Weak transcription	Colonic Mucosa	Colon
28	chr2:86248400-86252200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:86248400-86252600	Weak transcription	Fetal Intestine Large	intestine
30	chr2:86248400-86253000	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:86248400-86254200	Weak transcription	NHDF-Ad	bronchial
32	chr2:86248600-86252400	Weak transcription	NHLF	lung
33	chr2:86248600-86252800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:86248600-86252800	Weak transcription	Right Ventricle	heart
35	chr2:86248600-86253000	Weak transcription	Fetal Lung	lung
36	chr2:86248800-86252200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:86248800-86252400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:86248800-86252400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:86248800-86252400	Weak transcription	Adipose Nuclei	Adipose
40	chr2:86248800-86252600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:86248800-86252600	Weak transcription	Aorta	Aorta
42	chr2:86248800-86252600	Weak transcription	Left Ventricle	heart
43	chr2:86248800-86252600	Weak transcription	Ovary	ovary
44	chr2:86248800-86252600	Weak transcription	Pancreas	Pancrea
45	chr2:86248800-86252800	Weak transcription	Gastric	stomach
46	chr2:86248800-86257000	Weak transcription	Psoas Muscle	Psoas
47	chr2:86248800-86257200	Weak transcription	Fetal Kidney	kidney
48	chr2:86249000-86252200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:86249000-86252400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:86249000-86252400	Weak transcription	Brain Anterior Caudate	brain

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