Variant report

Variant	rs2299876
Chromosome Location	chr6:119537523-119537524
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	chr6:119537308..119539854-chr6:119540382..119542947,2	K562	blood:

Extended variants
information (count: 131 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1022868	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1022870	0.82[EUR][1000 genomes]
rs1022871	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10485000	0.89[CHB][hapmap]
rs10485001	0.86[GIH][hapmap];0.86[LWK][hapmap];0.80[TSI][hapmap]
rs10872175	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10872176	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11153796	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11153797	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11153800	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs11153804	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11153805	0.81[CEU][hapmap]
rs11153806	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11153807	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11153809	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11751945	0.81[CEU][hapmap];0.93[YRI][hapmap]
rs11759899	0.86[GIH][hapmap];0.80[TSI][hapmap]
rs11961647	0.82[EUR][1000 genomes]
rs12198423	0.80[AFR][1000 genomes]
rs12205826	0.81[CEU][hapmap]
rs17080912	0.89[CHB][hapmap]
rs17080974	0.89[CHB][hapmap]
rs17080980	0.89[CHB][hapmap]
rs17080995	0.89[CHB][hapmap]
rs17081019	0.89[CHB][hapmap]
rs17081022	0.89[CHB][hapmap]
rs17081026	0.89[CHB][hapmap]
rs17081029	0.89[CHB][hapmap]
rs17081031	0.89[CHB][hapmap]
rs17081044	0.89[CHB][hapmap]
rs17514051	0.80[EUR][1000 genomes]
rs1884180	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2038769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2299885	0.89[CHB][hapmap]
rs3778105	0.89[CHB][hapmap]
rs3778106	0.89[CHB][hapmap]
rs3778109	0.89[CHB][hapmap]
rs3798620	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798622	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798623	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798625	0.89[CHB][hapmap]
rs3798631	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798632	1.00[CHB][hapmap]
rs3798633	1.00[CHB][hapmap]
rs3798634	0.89[CHB][hapmap]
rs3798644	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3798645	0.89[CHB][hapmap]
rs3798646	0.89[CHB][hapmap]
rs3798647	0.89[CHB][hapmap]
rs3823000	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3823003	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3823005	0.86[CHB][hapmap]
rs3891271	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4409209	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4552766	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56763032	0.82[ASN][1000 genomes]
rs6420705	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6420706	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6420708	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6569067	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6569068	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6569069	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6569070	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6569071	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902335	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902669	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902792	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902889	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6903249	0.81[EUR][1000 genomes]
rs6911427	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6911753	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913626	0.82[EUR][1000 genomes]
rs6914447	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6915559	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6915947	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6918089	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6918093	0.88[CHB][hapmap]
rs6918913	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs6922559	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6923181	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6923755	0.88[CHB][hapmap]
rs6932292	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6934431	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6938540	0.83[EUR][1000 genomes]
rs715373	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs715374	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs763392	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7740043	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7741003	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7741954	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7743299	0.81[EUR][1000 genomes]
rs7743728	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7743979	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7744142	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7746867	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7750041	0.82[EUR][1000 genomes]
rs7750901	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7750941	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7753315	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7753492	0.81[AFR][1000 genomes]
rs7754289	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764238	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7770398	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7770777	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9320685	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9320686	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9481898	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9481900	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9481901	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489661	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489662	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489663	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489664	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489665	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489667	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9489668	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489669	0.95[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489670	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489671	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489672	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489673	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489674	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489675	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489679	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489680	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489681	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9489686	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1034992	chr6:119512657-119540895	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2299876	ASF1A	cis	cerebellum	SCAN
rs2299876	TREX2	trans	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119494600-119547400	Weak transcription	Esophagus	oesophagus
2	chr6:119503400-119539800	Weak transcription	Gastric	stomach
3	chr6:119519200-119558400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:119524800-119539000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:119524800-119558400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:119525400-119548600	Weak transcription	Aorta	Aorta
7	chr6:119525400-119556000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:119525400-119558400	Weak transcription	Small Intestine	intestine
9	chr6:119525800-119554200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:119525800-119555800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:119526000-119538800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:119526000-119555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:119526000-119558400	Weak transcription	Placenta	Placenta
14	chr6:119526200-119558400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:119528600-119551200	Weak transcription	Primary B cells from cord blood	blood
16	chr6:119531200-119552000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:119531600-119558400	Weak transcription	NHLF	lung
18	chr6:119535400-119538400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:119535600-119538200	Enhancers	Fetal Lung	lung
20	chr6:119535800-119537600	Enhancers	Adipose Nuclei	Adipose
21	chr6:119536200-119538400	Enhancers	Liver	Liver
22	chr6:119536400-119538200	Enhancers	Colon Smooth Muscle	Colon
23	chr6:119536400-119540000	Genic enhancers	HepG2	liver
24	chr6:119536600-119537600	Strong transcription	Primary hematopoietic stem cells	blood
25	chr6:119536600-119538200	Enhancers	Fetal Heart	heart
26	chr6:119536800-119541600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:119537000-119537600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:119537000-119537600	Enhancers	Right Ventricle	heart
29	chr6:119537000-119537800	Enhancers	Left Ventricle	heart
30	chr6:119537000-119537800	Enhancers	Ovary	ovary
31	chr6:119537000-119538600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:119537200-119537600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:119537200-119537600	Enhancers	Right Atrium	heart
34	chr6:119537200-119537600	Transcr. at gene 5' and 3'	K562	blood
35	chr6:119537200-119537800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:119537200-119545400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:119537400-119547400	Weak transcription	Pancreas	Pancrea
38	chr6:119537400-119550800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:119537400-119554000	Weak transcription	Fetal Intestine Large	intestine
40	chr6:119537400-119554000	Weak transcription	Fetal Intestine Small	intestine
41	chr6:119537400-119556800	Weak transcription	Fetal Stomach	stomach

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