Variant report

Variant	rs7623525
Chromosome Location	chr3:119024379-119024380
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	chr3:119023465..119026044-chr3:119041239..119043477,3	MCF-7	breast:
2	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10934489	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11914541	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4687993	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56269733	0.85[EUR][1000 genomes]
rs6438517	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6775982	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6800491	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7620780	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7622994	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7625392	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7640033	0.94[CEU][hapmap]
rs7649558	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119014200-119029800	Weak transcription	Gastric	stomach
2	chr3:119014200-119032800	Weak transcription	Pancreas	Pancrea
3	chr3:119015000-119028600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:119015000-119041200	Weak transcription	Aorta	Aorta
5	chr3:119015200-119041000	Weak transcription	Fetal Kidney	kidney
6	chr3:119015800-119024400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:119015800-119024400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:119016000-119035400	Weak transcription	Fetal Brain Male	brain
9	chr3:119016000-119041000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:119016400-119040800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:119016400-119041000	Weak transcription	Fetal Intestine Small	intestine
12	chr3:119016600-119024400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:119016600-119025000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:119016800-119024800	Enhancers	Fetal Heart	heart
15	chr3:119017200-119025000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:119017400-119029800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:119017400-119040600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr3:119017600-119032400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:119018800-119032800	Weak transcription	Thymus	Thymus
20	chr3:119019200-119024800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:119019200-119024800	Genic enhancers	Fetal Stomach	stomach
22	chr3:119019200-119026000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:119019200-119040800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:119019600-119024800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:119020200-119024400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:119020400-119029800	Weak transcription	Colonic Mucosa	Colon
27	chr3:119020400-119040600	Weak transcription	Esophagus	oesophagus
28	chr3:119020800-119030400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:119020800-119032400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:119021000-119027200	Weak transcription	Brain Substantia Nigra	brain
31	chr3:119021000-119030400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:119021000-119032400	Weak transcription	Primary T cells from cord blood	blood
33	chr3:119021200-119041000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:119021200-119041000	Weak transcription	Fetal Thymus	thymus
35	chr3:119021600-119024800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr3:119021600-119024800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:119021600-119024800	Enhancers	Right Atrium	heart
38	chr3:119021600-119025000	Enhancers	HSMMtube	muscle
39	chr3:119021800-119024400	Genic enhancers	Fetal Muscle Leg	muscle
40	chr3:119022000-119024800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:119022000-119025800	Enhancers	NH-A	brain
42	chr3:119022000-119026200	Enhancers	HSMM	muscle
43	chr3:119022000-119032400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:119022200-119024800	Enhancers	Adipose Nuclei	Adipose
45	chr3:119022200-119029000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:119022200-119040800	Weak transcription	Brain Angular Gyrus	brain
47	chr3:119022400-119024400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:119022400-119024400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:119022400-119024600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:119022400-119025000	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links