Variant report

Variant	rs3795139
Chromosome Location	chr20:1285933-1285934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1279418..1283217-chr20:1283449..1287758,5	K562	blood:
2	chr20:1285641..1287786-chr20:1289716..1291902,2	K562	blood:
3	chr20:1283698..1286846-chr20:1286878..1289632,3	K562	blood:

Variant related genes	Relation type
ENSG00000125775	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12624336	0.88[ASN][1000 genomes]
rs2317645	0.91[JPT][hapmap]
rs3752306	0.95[ASN][1000 genomes]
rs3764715	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3795140	0.92[ASN][1000 genomes]
rs3795141	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3795142	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3818331	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6109320	0.86[JPT][hapmap]
rs6134520	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1067393	chr20:1254805-1302796	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv912588	chr20:1269588-1300456	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv912589	chr20:1272686-1298397	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv912590	chr20:1278770-1298397	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv912591	chr20:1283523-1296811	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
8	nsv912592	chr20:1283523-1297516	Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
9	nsv912593	chr20:1283523-1298397	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv912594	chr20:1283523-1299968	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv912595	chr20:1283523-1313762	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1272200-1286000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr20:1272600-1294000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr20:1273000-1294000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr20:1274800-1288200	Weak transcription	Fetal Intestine Small	intestine
5	chr20:1275000-1289400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:1275800-1293800	Weak transcription	Brain Substantia Nigra	brain
7	chr20:1276600-1289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr20:1278200-1294000	Weak transcription	Colon Smooth Muscle	Colon
9	chr20:1280600-1294000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr20:1281400-1289800	Weak transcription	Colonic Mucosa	Colon
11	chr20:1281600-1290000	Weak transcription	Brain Hippocampus Middle	brain
12	chr20:1281800-1294000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr20:1282000-1289000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:1282000-1293800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr20:1282000-1293800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr20:1282000-1294000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr20:1282000-1294400	Weak transcription	Stomach Mucosa	stomach
18	chr20:1282000-1298200	Weak transcription	A549	lung
19	chr20:1282200-1288800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr20:1282200-1289600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr20:1282200-1289800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr20:1282200-1293600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr20:1282200-1294000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr20:1282200-1294000	Weak transcription	NHDF-Ad	bronchial
25	chr20:1282200-1294000	Weak transcription	NHEK	skin
26	chr20:1282200-1298600	Weak transcription	Thymus	Thymus
27	chr20:1282400-1289400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr20:1282400-1294200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr20:1283400-1287200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr20:1283400-1287400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr20:1283400-1288000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr20:1283400-1288600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr20:1283400-1288800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr20:1283400-1289000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr20:1283400-1290000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr20:1283600-1286600	Strong transcription	Right Ventricle	heart
37	chr20:1283600-1287400	Strong transcription	Fetal Brain Female	brain
38	chr20:1283600-1287600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr20:1283800-1288000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr20:1283800-1301800	Weak transcription	HSMMtube	muscle
41	chr20:1284000-1294000	Weak transcription	Osteobl	bone
42	chr20:1284200-1286600	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr20:1284200-1287000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr20:1284200-1289400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr20:1284200-1303600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr20:1284400-1293200	Weak transcription	Brain Angular Gyrus	brain
47	chr20:1284600-1287200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr20:1284600-1288000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr20:1284600-1289200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr20:1284600-1290600	Strong transcription	Fetal Stomach	stomach

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