Variant report

Variant	rs10173899
Chromosome Location	chr2:153355512-153355513
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	chr2:153353996..153356046-chr2:153357031..153359533,2	K562	blood:
2	chr2:153345928..153348906-chr2:153354040..153356962,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10179418	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs10180542	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10194603	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10208776	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10432493	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12616906	0.83[ASN][1000 genomes]
rs12693378	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13390698	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs13424038	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13427076	0.94[JPT][hapmap]
rs13427990	0.81[ASN][1000 genomes]
rs16831169	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831174	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2078444	0.81[ASN][1000 genomes]
rs2346205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2346209	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2881339	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4143274	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4146259	0.94[JPT][hapmap]
rs4664587	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4664589	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664590	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58121347	0.94[ASN][1000 genomes]
rs59965317	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434059	1.00[JPT][hapmap]
rs6434060	0.81[ASN][1000 genomes]
rs6434061	0.83[ASN][1000 genomes]
rs6434062	0.81[ASN][1000 genomes]
rs6725661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737699	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs6747765	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6748954	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs73002264	0.84[ASN][1000 genomes]
rs73968029	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7559217	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7582984	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7586195	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7587794	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7590207	0.83[ASN][1000 genomes]
rs7592283	0.82[ASN][1000 genomes]
rs7593411	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7594969	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7606592	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153342600-153355800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:153343000-153360600	Enhancers	Brain Anterior Caudate	brain
3	chr2:153348600-153357200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:153348800-153370200	Weak transcription	Aorta	Aorta
5	chr2:153350400-153357400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:153350800-153355800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:153350800-153357000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:153350800-153360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:153351000-153355600	Weak transcription	Fetal Stomach	stomach
10	chr2:153351400-153357600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:153351400-153361000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:153351600-153359600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:153352000-153359800	Enhancers	Brain Substantia Nigra	brain
14	chr2:153352200-153356000	Enhancers	Brain Hippocampus Middle	brain
15	chr2:153353400-153356400	Enhancers	HepG2	liver
16	chr2:153353600-153355600	Weak transcription	Fetal Brain Male	brain
17	chr2:153353600-153357000	Enhancers	Hela-S3	cervix
18	chr2:153353800-153356000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:153354000-153355800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:153354000-153356000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:153354200-153357200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:153354200-153357200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:153354200-153357200	Enhancers	Fetal Intestine Large	intestine
24	chr2:153354200-153357200	Enhancers	Fetal Intestine Small	intestine
25	chr2:153354200-153357200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr2:153354200-153358200	Enhancers	Adipose Nuclei	Adipose
27	chr2:153354200-153358800	Enhancers	Brain Angular Gyrus	brain
28	chr2:153354200-153360000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:153354400-153356200	Enhancers	Colon Smooth Muscle	Colon
30	chr2:153354400-153356400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:153354400-153356600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:153354400-153361000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:153354600-153355600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:153354600-153355600	Weak transcription	Colonic Mucosa	Colon
35	chr2:153354600-153355600	Weak transcription	Fetal Lung	lung
36	chr2:153354600-153355600	Weak transcription	Placenta	Placenta
37	chr2:153354600-153355600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:153354600-153355600	Weak transcription	Small Intestine	intestine
39	chr2:153354600-153355800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:153354600-153355800	Weak transcription	Right Atrium	heart
41	chr2:153354600-153355800	Weak transcription	Right Ventricle	heart
42	chr2:153354600-153355800	Weak transcription	Stomach Mucosa	stomach
43	chr2:153354600-153355800	Weak transcription	NHDF-Ad	bronchial
44	chr2:153354600-153355800	Weak transcription	NHEK	skin
45	chr2:153354600-153356000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr2:153354600-153360600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:153354600-153361000	Weak transcription	NHLF	lung
48	chr2:153354600-153364600	Weak transcription	Left Ventricle	heart
49	chr2:153354600-153365200	Weak transcription	Pancreas	Pancrea
50	chr2:153354800-153355600	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links