Variant report

Variant	rs4959648
Chromosome Location	chr6:2363692-2363693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:2351761..2353493-chr6:2362781..2364796,2	K562	blood:
2	chr6:2357336..2360924-chr6:2363674..2365844,4	K562	blood:
3	chr6:2362511..2364691-chr6:2394137..2395852,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1196389	0.93[CEU][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes]
rs1196390	0.89[AMR][1000 genomes]
rs1196393	0.89[AMR][1000 genomes]
rs1196396	0.85[AMR][1000 genomes]
rs1475411	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1486274	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1684153	0.89[AMR][1000 genomes]
rs1887418	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887420	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2148824	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234920	0.87[JPT][hapmap]
rs2450301	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2450303	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2450306	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2450311	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2478999	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2479000	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2479003	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2479005	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479009	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479010	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2479012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479015	0.81[GIH][hapmap];0.93[JPT][hapmap];0.83[MKK][hapmap]
rs2505656	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505665	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505668	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505669	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2505674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335963	0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes]
rs4959171	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62392643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6596876	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6939099	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7765735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328086	0.85[CEU][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes]
rs9392379	0.85[AMR][1000 genomes]
rs9392382	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9405552	0.84[AMR][1000 genomes]
rs9501828	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2339200-2370000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:2344400-2377400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:2345400-2365800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:2352400-2376400	Weak transcription	HSMMtube	muscle
5	chr6:2353800-2376400	Weak transcription	Pancreas	Pancrea
6	chr6:2354200-2366800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:2354200-2367200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:2354200-2371600	Weak transcription	Right Ventricle	heart
9	chr6:2354200-2376400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:2356200-2369800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:2356200-2382200	Weak transcription	Aorta	Aorta
12	chr6:2356600-2382800	Weak transcription	Psoas Muscle	Psoas
13	chr6:2357000-2363800	Weak transcription	Brain Anterior Caudate	brain
14	chr6:2358000-2370000	Weak transcription	Esophagus	oesophagus
15	chr6:2358600-2363800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:2358800-2364000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:2359000-2365000	Weak transcription	Gastric	stomach
18	chr6:2360400-2379600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:2361400-2370000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:2362200-2370600	Weak transcription	Fetal Stomach	stomach
21	chr6:2362400-2364000	Weak transcription	Primary B cells from cord blood	blood
22	chr6:2362400-2371400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:2362400-2376800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:2362400-2391800	Weak transcription	Fetal Intestine Small	intestine
25	chr6:2362400-2397200	Weak transcription	Liver	Liver
26	chr6:2362600-2364400	Weak transcription	Fetal Intestine Large	intestine
27	chr6:2362600-2367200	Weak transcription	Ovary	ovary
28	chr6:2362800-2397200	Weak transcription	Left Ventricle	heart
29	chr6:2363000-2365000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:2363200-2363800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:2363600-2366800	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links