Variant report

Variant	rs10456117
Chromosome Location	chr6:12577399-12577400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16873037	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2490450	0.96[AFR][1000 genomes]
rs2490451	0.95[AFR][1000 genomes]
rs2504890	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504891	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504894	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516236	1.00[TSI][hapmap]
rs60010784	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv470801	chr6:12559239-12666093	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv462638	chr6:12569231-12651249	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv600991	chr6:12569231-12651249	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12569800-12577400	Weak transcription	Esophagus	oesophagus
2	chr6:12573200-12579200	Enhancers	NHDF-Ad	bronchial
3	chr6:12573800-12577600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:12573800-12578800	Enhancers	HUVEC	blood vessel
5	chr6:12573800-12579400	Enhancers	HSMM	muscle
6	chr6:12573800-12586000	Weak transcription	Pancreas	Pancrea
7	chr6:12574000-12577400	Weak transcription	Placenta	Placenta
8	chr6:12574000-12577800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:12574000-12578000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:12574000-12578200	Enhancers	HSMMtube	muscle
11	chr6:12574000-12579400	Enhancers	A549	lung
12	chr6:12574000-12594600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:12575600-12577800	Enhancers	Fetal Brain Male	brain
14	chr6:12575600-12578200	Enhancers	Fetal Intestine Large	intestine
15	chr6:12575600-12581200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:12575800-12578200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr6:12576000-12579000	Enhancers	Fetal Intestine Small	intestine
18	chr6:12576000-12580200	Enhancers	HMEC	breast
19	chr6:12576200-12579000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:12576200-12579200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:12576400-12579400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr6:12576600-12578800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:12576800-12578800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:12576800-12579200	Enhancers	Osteobl	bone
25	chr6:12576800-12579400	Enhancers	NH-A	brain
26	chr6:12576800-12579600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:12576800-12580000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:12577000-12579200	Enhancers	NHLF	lung
29	chr6:12577000-12580200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr6:12577200-12577400	Bivalent Enhancer	Fetal Heart	heart
31	chr6:12577200-12577600	Enhancers	Duodenum Mucosa	Duodenum
32	chr6:12577200-12577600	Enhancers	Fetal Kidney	kidney
33	chr6:12577200-12577600	Enhancers	NHEK	skin
34	chr6:12577200-12578200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links