Variant report

Variant	rs2819852
Chromosome Location	chr6:45417663-45417664
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:45412131..45416669-chr6:45417302..45422043,11	K562	blood:
2	chr6:45415340..45418942-chr6:45422164..45424791,5	K562	blood:
3	chr6:45416242..45417772-chr6:45424221..45426161,2	MCF-7	breast:
4	chr6:45409836..45411683-chr6:45415298..45417757,2	K562	blood:
5	chr6:45412401..45414815-chr6:45415090..45418058,3	K562	blood:
6	chr6:45415640..45418079-chr6:45419010..45422483,4	MCF-7	breast:
7	chr6:45416687..45419671-chr6:45507233..45509746,2	K562	blood:
8	chr6:45344177..45348784-chr6:45412133..45417901,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10214519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12210100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12215249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1316330	1.00[CHB][hapmap]
rs1317777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13208741	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1343799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934327	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2252718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2256819	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396442	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2677098	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790094	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2790097	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790099	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790102	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819865	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819866	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2819867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711816	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756144	0.90[EUR][1000 genomes]
rs910586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9472494	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9885645	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[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	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

No data

Chromatin state (count:66 , 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	chr6:45407200-45418200	Weak transcription	Gastric	stomach
3	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:45413400-45423400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:45413800-45418000	Weak transcription	Primary T cells from cord blood	blood
6	chr6:45413800-45418000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:45414000-45421400	Weak transcription	Esophagus	oesophagus
8	chr6:45414000-45431400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:45414200-45417800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:45414200-45418000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:45414200-45418000	Weak transcription	Fetal Intestine Large	intestine
12	chr6:45414200-45419000	Enhancers	K562	blood
13	chr6:45414400-45420000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:45414800-45418200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:45415000-45421000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:45415000-45421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:45415200-45421800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:45415200-45421800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:45415200-45422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:45415200-45422200	Weak transcription	HMEC	breast
21	chr6:45415600-45419200	Enhancers	Fetal Thymus	thymus
22	chr6:45415600-45424600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:45415800-45419000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr6:45415800-45420000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:45415800-45421800	Weak transcription	NHEK	skin
26	chr6:45416000-45417800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:45416000-45420800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr6:45416000-45421800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:45416200-45420000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:45416200-45421800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr6:45416400-45417800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:45416400-45419400	Weak transcription	Colonic Mucosa	Colon
33	chr6:45416400-45421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:45416400-45421200	Weak transcription	HUVEC	blood vessel
35	chr6:45416400-45421800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:45416400-45430600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:45416400-45440400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:45416600-45418000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:45416600-45418200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:45416600-45430000	Weak transcription	Small Intestine	intestine
41	chr6:45416800-45418000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:45416800-45418400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:45416800-45418600	Strong transcription	Primary hematopoietic stem cells	blood
44	chr6:45416800-45420600	Strong transcription	NH-A	brain
45	chr6:45417000-45418400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:45417200-45419400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr6:45417200-45419400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:45417200-45419800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr6:45417200-45421200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:45417200-45421400	Weak transcription	Duodenum Mucosa	Duodenum

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