Variant report

Variant	rs17748452
Chromosome Location	chr6:53687279-53687280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10498795	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1543356	1.00[CEU][hapmap]
rs16884427	0.80[AMR][1000 genomes]
rs2223617	1.00[CEU][hapmap]
rs2820217	1.00[CEU][hapmap]
rs2820218	1.00[CEU][hapmap]
rs4276504	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4357137	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4380749	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4397225	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4476827	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4580851	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6905927	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6908101	0.83[EUR][1000 genomes]
rs6925165	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs761135	0.89[CEU][hapmap]
rs7752696	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9474672	1.00[CEU][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:53678600-53692200	Weak transcription	Esophagus	oesophagus
5	chr6:53680400-53690000	Weak transcription	Fetal Intestine Small	intestine
6	chr6:53680400-53690200	Weak transcription	Fetal Thymus	thymus
7	chr6:53680400-53691800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:53680400-53692400	Weak transcription	Pancreas	Pancrea
9	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:53680600-53689400	Weak transcription	Fetal Intestine Large	intestine
11	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:53680800-53689600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:53681200-53689800	Weak transcription	Osteobl	bone
14	chr6:53682600-53689400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:53683600-53689800	Weak transcription	Dnd41	blood
16	chr6:53684000-53687400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:53684000-53687600	Weak transcription	Psoas Muscle	Psoas
18	chr6:53684000-53691400	Weak transcription	Hela-S3	cervix
19	chr6:53684000-53692400	Weak transcription	Left Ventricle	heart
20	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
22	chr6:53684200-53689400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:53684600-53690600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
25	chr6:53684800-53688200	Enhancers	Brain Cingulate Gyrus	brain
26	chr6:53684800-53689800	Weak transcription	HMEC	breast
27	chr6:53685000-53689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:53685000-53689800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:53685000-53690200	Weak transcription	NHEK	skin
30	chr6:53685200-53688000	Enhancers	Brain Anterior Caudate	brain
31	chr6:53685600-53688400	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr6:53685800-53687600	Enhancers	Colon Smooth Muscle	Colon
33	chr6:53685800-53688000	Enhancers	Brain Angular Gyrus	brain
34	chr6:53686000-53690400	Weak transcription	Gastric	stomach
35	chr6:53686200-53687800	Enhancers	Rectal Smooth Muscle	rectum
36	chr6:53686400-53688000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:53686800-53687400	Enhancers	Right Atrium	heart
38	chr6:53686800-53687600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:53686800-53687600	Enhancers	Stomach Smooth Muscle	stomach
40	chr6:53686800-53687800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr6:53686800-53688000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:53687000-53687400	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr6:53687000-53687400	Enhancers	Stomach Mucosa	stomach
44	chr6:53687000-53687600	Enhancers	Fetal Heart	heart
45	chr6:53687000-53687800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:53687000-53687800	Enhancers	Fetal Brain Female	brain
47	chr6:53687000-53687800	Enhancers	HepG2	liver
48	chr6:53687200-53687400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr6:53687200-53687600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:53687200-53687600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links