Variant report

Variant	rs2820339
Chromosome Location	chr6:45419110-45419111
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45412131..45416669-chr6:45417302..45422043,11	K562	blood:
2	chr6:45415640..45418079-chr6:45419010..45422483,4	MCF-7	breast:
3	chr6:45416687..45419671-chr6:45507233..45509746,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10214519	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs12197948	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs12210100	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12215249	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs12665622	0.81[CHD][hapmap]
rs1317777	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1343799	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1934327	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2252718	1.00[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs2396442	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2677098	1.00[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs2677099	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs2677100	0.98[EUR][1000 genomes]
rs2677109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2677110	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2790093	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2790094	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2790095	0.92[EUR][1000 genomes]
rs2790097	0.92[EUR][1000 genomes]
rs2790098	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2790099	0.92[EUR][1000 genomes]
rs2790100	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2790102	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790103	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2819852	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2819853	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs2819861	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs2819864	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2819865	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2819866	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2819867	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4711816	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs6458443	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6905689	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs73448153	0.80[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7751050	0.82[JPT][hapmap]
rs7756144	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs910586	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs9472494	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs9885645	1.00[CEU][hapmap];0.93[EUR][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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2820339	RUNX2	cis	multi-tissue	Pritchard
rs2820339	MRPL2	cis	cerebellum	SCAN
rs2820339	KLHDC3	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:45413400-45423400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:45414000-45421400	Weak transcription	Esophagus	oesophagus
5	chr6:45414000-45431400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:45414400-45420000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:45415000-45421000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:45415000-45421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:45415200-45421800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:45415200-45421800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:45415200-45422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:45415200-45422200	Weak transcription	HMEC	breast
13	chr6:45415600-45419200	Enhancers	Fetal Thymus	thymus
14	chr6:45415600-45424600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:45415800-45420000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:45415800-45421800	Weak transcription	NHEK	skin
17	chr6:45416000-45420800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:45416000-45421800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:45416200-45420000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:45416200-45421800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:45416400-45419400	Weak transcription	Colonic Mucosa	Colon
22	chr6:45416400-45421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:45416400-45421200	Weak transcription	HUVEC	blood vessel
24	chr6:45416400-45421800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:45416400-45430600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:45416400-45440400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:45416600-45430000	Weak transcription	Small Intestine	intestine
28	chr6:45416800-45420600	Strong transcription	NH-A	brain
29	chr6:45417200-45419400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr6:45417200-45419400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:45417200-45419800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr6:45417200-45421200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr6:45417200-45421400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:45417200-45422400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:45417400-45419800	Enhancers	Dnd41	blood
36	chr6:45417400-45419800	Weak transcription	Hela-S3	cervix
37	chr6:45417400-45420600	Weak transcription	NHDF-Ad	bronchial
38	chr6:45417400-45420800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:45417400-45421200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:45417400-45421400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:45417400-45421400	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr6:45417400-45421800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:45417600-45419200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:45417600-45421200	Strong transcription	Osteobl	bone
45	chr6:45417600-45422200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:45417800-45419200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr6:45418000-45419200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:45418000-45420200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr6:45418000-45420200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:45418000-45420800	Enhancers	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links