Variant report

Variant	rs6539103
Chromosome Location	chr12:104253289-104253290
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104221407..104223311-chr12:104252551..104254594,2	MCF-7	breast:
2	chr12:104252726..104255857-chr12:104256920..104259686,3	MCF-7	breast:
3	chr12:104252627..104253426-chr6:163440642..163441162,2	MCF-7	breast:
4	chr12:104252720..104255183-chr12:104502836..104504925,2	K562	blood:
5	chr12:104234105..104239098-chr12:104250004..104255076,13	MCF-7	breast:
6	chr12:104247921..104249635-chr12:104251344..104253746,2	MCF-7	breast:
7	chr12:104164135..104167659-chr12:104253252..104255970,3	MCF-7	breast:
8	chr12:104250532..104253421-chr12:104255015..104257063,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10745984	0.95[ASN][1000 genomes]
rs10778292	0.95[ASN][1000 genomes]
rs10861130	0.95[ASN][1000 genomes]
rs10861131	0.95[ASN][1000 genomes]
rs11111815	0.95[ASN][1000 genomes]
rs11111831	0.95[ASN][1000 genomes]
rs12302488	0.95[ASN][1000 genomes]
rs12371102	0.95[ASN][1000 genomes]
rs2576969	0.87[ASN][1000 genomes]
rs3812801	0.95[ASN][1000 genomes]
rs7302036	0.87[ASN][1000 genomes]
rs7968124	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971317	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971563	0.95[ASN][1000 genomes]
rs9989004	0.95[ASN][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	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 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	chr12:104236000-104253600	Weak transcription	Gastric	stomach
2	chr12:104240000-104254800	Enhancers	Rectal Smooth Muscle	rectum
3	chr12:104246800-104254000	Weak transcription	Brain Anterior Caudate	brain
4	chr12:104250000-104257000	Weak transcription	Pancreas	Pancrea
5	chr12:104250000-104263800	Weak transcription	Liver	Liver
6	chr12:104250400-104254000	Weak transcription	Ovary	ovary
7	chr12:104251000-104253400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:104251200-104254400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:104251400-104254400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:104252000-104254000	Enhancers	HSMMtube	muscle
11	chr12:104252000-104254400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:104252200-104254400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:104252200-104254400	Enhancers	HSMM	muscle
14	chr12:104252200-104254600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:104252200-104254800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:104252200-104254800	Enhancers	Stomach Smooth Muscle	stomach
17	chr12:104252200-104255000	Enhancers	HMEC	breast
18	chr12:104252200-104255800	Enhancers	Placenta	Placenta
19	chr12:104252400-104253800	Enhancers	Fetal Intestine Large	intestine
20	chr12:104252400-104254000	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr12:104252400-104254000	Enhancers	NH-A	brain
22	chr12:104252400-104254200	Enhancers	NHLF	lung
23	chr12:104252400-104254400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:104252400-104254400	Enhancers	NHDF-Ad	bronchial
25	chr12:104252400-104255000	Enhancers	Colon Smooth Muscle	Colon
26	chr12:104252600-104253400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr12:104252600-104253600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:104252600-104253800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:104252600-104253800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:104252600-104253800	Enhancers	Fetal Intestine Small	intestine
31	chr12:104252600-104253800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:104252600-104253800	Enhancers	HUVEC	blood vessel
33	chr12:104252600-104253800	Enhancers	K562	blood
34	chr12:104252600-104254000	Enhancers	Osteobl	bone
35	chr12:104252600-104254400	Enhancers	Esophagus	oesophagus
36	chr12:104252600-104254400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr12:104252600-104254800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:104252600-104255000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:104252800-104253600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr12:104252800-104253800	Enhancers	Stomach Mucosa	stomach
41	chr12:104252800-104254400	Enhancers	Fetal Stomach	stomach
42	chr12:104253000-104253400	Enhancers	HepG2	liver
43	chr12:104253000-104254400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:104253200-104253400	Flanking Active TSS	NHEK	skin
45	chr12:104253200-104253600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:104253200-104253600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:104253200-104253600	Flanking Active TSS	A549	lung
48	chr12:104253200-104254200	Flanking Active TSS	Hela-S3	cervix
49	chr12:104253200-104254800	Enhancers	Placenta Amnion	Placenta Amnion

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