Variant report

Variant	rs6109437
Chromosome Location	chr20:1301598-1301599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1299694..1302463-chr20:1372805..1375416,2	MCF-7	breast:
2	chr20:1301486..1304353-chr20:1304834..1307376,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234684	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11087048	1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11699494	1.00[CHB][hapmap]
rs13163	1.00[CHB][hapmap]
rs13433171	1.00[ASN][1000 genomes]
rs16994239	1.00[CHB][hapmap]
rs16994549	1.00[CHB][hapmap]
rs17793560	1.00[CHB][hapmap]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2873522	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4577347	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs4813115	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4814102	1.00[CHB][hapmap]
rs56035174	1.00[ASN][1000 genomes]
rs57806058	1.00[ASN][1000 genomes]
rs59377624	1.00[ASN][1000 genomes]
rs59681252	1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6033660	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033672	1.00[ASN][1000 genomes]
rs6033871	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6033896	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap]
rs6041382	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6041689	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6042000	1.00[ASN][1000 genomes]
rs6042506	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6042550	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6042574	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6042578	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6105101	1.00[CHB][hapmap]
rs6109511	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6109522	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109740	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6109784	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6110189	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6110193	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs62187542	1.00[ASN][1000 genomes]
rs62187543	1.00[ASN][1000 genomes]
rs6514337	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6514364	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs715217	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs73067251	1.00[ASN][1000 genomes]
rs73069188	1.00[ASN][1000 genomes]
rs73579382	1.00[ASN][1000 genomes]
rs73581208	1.00[ASN][1000 genomes]
rs747611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8117563	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8117744	1.00[ASN][1000 genomes]
rs8118276	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8119259	1.00[ASN][1000 genomes]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1283800-1301800	Weak transcription	HSMMtube	muscle
2	chr20:1284200-1303600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:1289600-1305000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr20:1293400-1302200	Weak transcription	Esophagus	oesophagus
5	chr20:1294200-1301600	Weak transcription	Spleen	Spleen
6	chr20:1294200-1302000	Weak transcription	Gastric	stomach
7	chr20:1294200-1302200	Weak transcription	Pancreas	Pancrea
8	chr20:1294200-1305600	Weak transcription	Ovary	ovary
9	chr20:1294400-1301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr20:1294400-1304800	Weak transcription	Placenta	Placenta
11	chr20:1294600-1302800	Weak transcription	NHEK	skin
12	chr20:1294600-1305200	Weak transcription	Colon Smooth Muscle	Colon
13	chr20:1294600-1305200	Weak transcription	Fetal Thymus	thymus
14	chr20:1294600-1305400	Weak transcription	Colonic Mucosa	Colon
15	chr20:1294800-1302200	Weak transcription	Adipose Nuclei	Adipose
16	chr20:1294800-1305200	Weak transcription	Dnd41	blood
17	chr20:1295000-1302200	Weak transcription	Stomach Mucosa	stomach
18	chr20:1295000-1302200	Weak transcription	HUVEC	blood vessel
19	chr20:1296000-1301800	Strong transcription	Fetal Intestine Small	intestine
20	chr20:1298600-1302800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr20:1298600-1302800	Weak transcription	NHLF	lung
22	chr20:1298600-1305000	Weak transcription	A549	lung
23	chr20:1298800-1302200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr20:1298800-1303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:1298800-1303200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:1298800-1303800	Weak transcription	Hela-S3	cervix
27	chr20:1299000-1302000	Weak transcription	Liver	Liver
28	chr20:1299000-1302800	Weak transcription	NHDF-Ad	bronchial
29	chr20:1299000-1303200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr20:1299000-1305200	Weak transcription	GM12878-XiMat	blood
31	chr20:1299800-1304600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr20:1300000-1302800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr20:1300200-1301600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr20:1300200-1301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr20:1300200-1303000	Weak transcription	NH-A	brain
36	chr20:1300200-1303000	Weak transcription	Osteobl	bone
37	chr20:1300400-1301600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:1300400-1301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr20:1300400-1302000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr20:1300400-1305200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr20:1300600-1302800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr20:1300800-1301800	Weak transcription	Lung	lung
43	chr20:1300800-1302000	Weak transcription	Left Ventricle	heart
44	chr20:1300800-1303000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr20:1300800-1305400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr20:1301000-1305200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr20:1301000-1305600	Weak transcription	Fetal Intestine Large	intestine
48	chr20:1301200-1301800	Enhancers	HepG2	liver
49	chr20:1301200-1303000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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