Variant report

Variant	rs2292518
Chromosome Location	chr3:111445546-111445547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1105448	0.82[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12494734	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13061461	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13083322	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs13086018	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs1398751	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1398753	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1398754	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16858448	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs17423838	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs17489748	0.92[YRI][hapmap]
rs2137595	0.82[JPT][hapmap]
rs2292516	0.84[YRI][hapmap]
rs2399394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4401340	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4413291	0.82[JPT][hapmap]
rs4414820	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682298	0.86[JPT][hapmap]
rs66539950	0.82[AFR][1000 genomes]
rs7624162	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7646161	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7646453	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs938219	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9854875	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
2	chr3:111420400-111450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:111420600-111445600	Weak transcription	HepG2	liver
4	chr3:111427200-111448400	Weak transcription	Right Ventricle	heart
5	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:111429400-111446800	Weak transcription	Fetal Intestine Large	intestine
8	chr3:111431600-111451400	Weak transcription	Gastric	stomach
9	chr3:111432000-111448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:111432000-111448600	Weak transcription	Brain Germinal Matrix	brain
11	chr3:111433800-111447000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:111435200-111447800	Weak transcription	HUVEC	blood vessel
14	chr3:111436800-111448400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:111440400-111448400	Weak transcription	Right Atrium	heart
16	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
17	chr3:111441400-111448400	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
21	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
22	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:111442200-111445600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:111442400-111456000	Weak transcription	Lung	lung
26	chr3:111442600-111446600	Weak transcription	Fetal Heart	heart
27	chr3:111442600-111448400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:111442800-111446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:111442800-111447200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:111442800-111447200	Weak transcription	NHEK	skin
32	chr3:111442800-111448000	Weak transcription	Hela-S3	cervix
33	chr3:111442800-111448200	Weak transcription	Adipose Nuclei	Adipose
34	chr3:111442800-111448400	Weak transcription	Fetal Stomach	stomach
35	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:111443000-111447000	Weak transcription	NH-A	brain
37	chr3:111443000-111447200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:111443000-111447400	Weak transcription	HMEC	breast
39	chr3:111443000-111447400	Weak transcription	HSMM	muscle
40	chr3:111443000-111448000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:111443000-111448400	Weak transcription	Left Ventricle	heart
42	chr3:111443000-111448400	Weak transcription	Ovary	ovary
43	chr3:111443000-111448400	Weak transcription	A549	lung
44	chr3:111443200-111448000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:111443200-111448000	Weak transcription	NHDF-Ad	bronchial
46	chr3:111443200-111448200	Weak transcription	NHLF	lung
47	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
48	chr3:111443400-111448000	Weak transcription	Osteobl	bone
49	chr3:111443400-111448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:111443600-111448000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links