Variant report

Variant	rs10934104
Chromosome Location	chr3:111449789-111449790
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	chr3:111448045..111449995-chr3:111576976..111579247,2	MCF-7	breast:
2	chr3:111448469..111451104-chr3:111452736..111455582,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11709591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12638437	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398752	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398755	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513332	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1513333	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1513334	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399395	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs35840064	0.83[AMR][1000 genomes]
rs35894167	0.83[AMR][1000 genomes]
rs4450776	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4682055	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682297	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682300	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682301	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57628489	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60556634	0.83[AMR][1000 genomes]
rs6438002	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768082	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791600	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs6800228	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620801	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7636559	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7640416	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642808	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643067	0.91[AMR][1000 genomes]
rs7644696	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7648126	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650348	1.00[CEU][hapmap]
rs7651391	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs7653881	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951338	1.00[CEU][hapmap];0.85[YRI][hapmap]

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:60 , 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	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:111431600-111451400	Weak transcription	Gastric	stomach
6	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
8	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
11	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
12	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:111442400-111456000	Weak transcription	Lung	lung
15	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
18	chr3:111443800-111451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
20	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:111446800-111450200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:111447200-111451200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:111447200-111451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:111447400-111450200	Enhancers	HMEC	breast
25	chr3:111447400-111451000	Weak transcription	Fetal Intestine Large	intestine
26	chr3:111447600-111450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:111447600-111451000	Weak transcription	Stomach Mucosa	stomach
28	chr3:111447800-111451200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:111448000-111449800	Enhancers	NHDF-Ad	bronchial
30	chr3:111448400-111449800	Enhancers	Left Ventricle	heart
31	chr3:111448400-111450000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr3:111448600-111451200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:111448800-111449800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:111448800-111453600	Weak transcription	Right Atrium	heart
35	chr3:111448800-111454200	Weak transcription	Adipose Nuclei	Adipose
36	chr3:111449000-111453400	Weak transcription	Fetal Heart	heart
37	chr3:111449000-111453600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:111449000-111453600	Weak transcription	HUVEC	blood vessel
39	chr3:111449000-111454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:111449000-111455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:111449200-111450200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:111449200-111450800	Weak transcription	A549	lung
43	chr3:111449200-111453600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:111449200-111453600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:111449400-111449800	Flanking Active TSS	NHEK	skin
46	chr3:111449400-111451000	Weak transcription	Fetal Kidney	kidney
47	chr3:111449400-111451200	Weak transcription	Fetal Stomach	stomach
48	chr3:111449400-111453400	Weak transcription	HSMMtube	muscle
49	chr3:111449400-111456000	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:111449600-111450600	Weak transcription	HepG2	liver

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