Variant report

Variant	rs1014740
Chromosome Location	chr6:56269927-56269928
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	chr6:56263868..56266502-chr6:56269861..56271738,2	MCF-7	breast:
2	chr6:56268256..56270109-chr6:56270332..56272934,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1008768	0.95[CHB][hapmap];0.96[JPT][hapmap];0.91[ASN][1000 genomes]
rs1008769	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1008770	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1018414	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1018415	0.95[CHB][hapmap];0.96[JPT][hapmap];0.91[ASN][1000 genomes]
rs11968073	0.95[CHB][hapmap];0.96[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12205291	0.89[ASN][1000 genomes]
rs12528936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206552	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2143349	0.85[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2179519	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2206528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2206530	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2397222	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2894836	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35253323	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715621	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4715624	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629057	0.97[ASN][1000 genomes]
rs629506	0.97[ASN][1000 genomes]
rs643246	0.96[ASN][1000 genomes]
rs646884	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs669656	0.97[ASN][1000 genomes]
rs669728	0.97[ASN][1000 genomes]
rs926530	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9296843	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9349821	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370527	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9370530	1.00[CHB][hapmap];0.96[JPT][hapmap];0.96[ASN][1000 genomes]
rs9382625	0.82[ASN][1000 genomes]
rs9382627	0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9382630	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9396208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396209	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9942454	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1022577	chr6:56263674-56289698	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56253000-56282600	Weak transcription	Aorta	Aorta
2	chr6:56265200-56270000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:56265200-56270200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:56265200-56271200	Weak transcription	Stomach Mucosa	stomach
5	chr6:56265400-56270000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:56265400-56270000	Weak transcription	Gastric	stomach
7	chr6:56267200-56271800	Enhancers	HepG2	liver
8	chr6:56267800-56270000	Enhancers	Colon Smooth Muscle	Colon
9	chr6:56268000-56270400	Enhancers	Rectal Smooth Muscle	rectum
10	chr6:56268200-56270000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:56268400-56270000	Enhancers	Fetal Lung	lung
12	chr6:56268400-56270400	Enhancers	Liver	Liver
13	chr6:56268400-56270400	Enhancers	Fetal Stomach	stomach
14	chr6:56268400-56271400	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr6:56268600-56271600	Enhancers	Hela-S3	cervix
16	chr6:56268800-56270200	Weak transcription	Small Intestine	intestine
17	chr6:56269000-56270000	Weak transcription	Ovary	ovary
18	chr6:56269000-56270000	Weak transcription	Psoas Muscle	Psoas
19	chr6:56269000-56271400	Weak transcription	Fetal Heart	heart
20	chr6:56269200-56270000	Enhancers	A549	lung
21	chr6:56269200-56270600	Enhancers	Fetal Intestine Large	intestine
22	chr6:56269200-56270600	Enhancers	Fetal Intestine Small	intestine
23	chr6:56269200-56272600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:56269400-56270400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:56269400-56270600	Enhancers	Duodenum Mucosa	Duodenum

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