Variant report

Variant	rs343180
Chromosome Location	chr4:121769522-121769523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:121763712..121766459-chr4:121767957..121770236,3	MCF-7	breast:
2	chr4:121769272..121771821-chr4:121774320..121777055,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12501569	0.84[ASN][1000 genomes]
rs1376109	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1397772	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1450459	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1450472	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1450473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1450475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1511314	0.86[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs1530799	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs171069	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs180730	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs180731	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1839485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs184668	0.85[ASN][1000 genomes]
rs184669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1901136	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2034482	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2167207	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2597544	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2597546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597548	0.80[ASN][1000 genomes]
rs2597552	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667175	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2667176	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2667191	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3106313	0.85[ASN][1000 genomes]
rs3114955	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3115312	0.85[ASN][1000 genomes]
rs3115314	0.85[ASN][1000 genomes]
rs343166	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs343178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs343195	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs343197	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs343198	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs343200	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs343201	0.82[CHB][hapmap]
rs343202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343204	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343206	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343209	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs343211	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343212	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4833187	0.86[ASN][1000 genomes]
rs4833694	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs72680434	0.86[ASN][1000 genomes]
rs72680442	0.84[ASN][1000 genomes]
rs870252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1013704	chr4:121657648-121791601	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121729600-121770400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:121755800-121774600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr4:121756800-121779800	Weak transcription	Aorta	Aorta
4	chr4:121758200-121770400	Weak transcription	HSMM	muscle
5	chr4:121758200-121774600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:121759600-121775400	Weak transcription	Gastric	stomach
7	chr4:121760400-121775800	Weak transcription	Lung	lung
8	chr4:121761200-121778200	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:121761200-121783600	Weak transcription	Pancreas	Pancrea
10	chr4:121761400-121774600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:121761400-121777600	Weak transcription	Left Ventricle	heart
12	chr4:121763400-121778800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:121763600-121776600	Weak transcription	Fetal Stomach	stomach
14	chr4:121763800-121769800	Weak transcription	Osteobl	bone
15	chr4:121763800-121770400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:121763800-121771000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:121763800-121776600	Weak transcription	Fetal Heart	heart
18	chr4:121764000-121770000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:121764400-121769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:121765800-121786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:121766000-121776600	Weak transcription	Fetal Intestine Small	intestine
22	chr4:121766000-121786600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:121766200-121769600	Weak transcription	NHDF-Ad	bronchial
24	chr4:121766200-121790800	Weak transcription	Ovary	ovary
25	chr4:121766400-121776600	Weak transcription	Fetal Intestine Large	intestine
26	chr4:121768800-121769800	Weak transcription	Fetal Lung	lung
27	chr4:121769000-121774600	Weak transcription	Fetal Kidney	kidney
28	chr4:121769000-121779600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:121769200-121779600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:121769400-121770800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links