Variant report

Variant	rs12249305
Chromosome Location	chr10:28342740-28342741
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10508729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508730	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs11006804	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11006808	0.85[ASN][1000 genomes]
rs11006811	0.94[ASN][1000 genomes]
rs11006874	1.00[CEU][hapmap]
rs12241297	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12244891	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12246891	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12255657	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12266822	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12268684	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12268764	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12412297	0.84[ASN][1000 genomes]
rs17831032	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs17831062	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs1937806	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253165	0.91[ASN][1000 genomes]
rs2368290	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3780856	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780857	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780858	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802518	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802520	0.92[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs3802521	0.85[MKK][hapmap]
rs3802522	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57575764	0.81[ASN][1000 genomes]
rs58270577	0.84[ASN][1000 genomes]
rs60563943	0.81[ASN][1000 genomes]
rs6481498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs73606064	0.84[ASN][1000 genomes]
rs73606068	0.81[ASN][1000 genomes]
rs74127187	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7903206	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7919932	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7921547	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv831815	chr10:28235661-28407533	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1052182	chr10:28259142-28361830	Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv831816	chr10:28304698-28493635	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv894988	chr10:28337570-28410989	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv466855	chr10:28341783-28400835	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv550284	chr10:28341783-28400835	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28330000-28345000	Weak transcription	Pancreas	Pancrea
2	chr10:28331200-28345000	Weak transcription	Aorta	Aorta
3	chr10:28335000-28345800	Weak transcription	Brain Angular Gyrus	brain
4	chr10:28335600-28345000	Weak transcription	Fetal Stomach	stomach
5	chr10:28336200-28349400	Weak transcription	Gastric	stomach
6	chr10:28336400-28346000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr10:28336600-28345600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:28336800-28346600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr10:28337400-28347400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:28337800-28345000	Weak transcription	Fetal Intestine Small	intestine
11	chr10:28337800-28346000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:28338200-28345000	Weak transcription	Left Ventricle	heart
13	chr10:28338400-28345000	Weak transcription	Esophagus	oesophagus
14	chr10:28339000-28345000	Weak transcription	Lung	lung
15	chr10:28339800-28345000	Weak transcription	Primary T cells from cord blood	blood
16	chr10:28341200-28350000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr10:28341200-28377600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr10:28341400-28346400	Weak transcription	Spleen	Spleen
19	chr10:28341800-28348600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr10:28341800-28349000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr10:28341800-28349800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr10:28342200-28345000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:28342400-28342800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr10:28342400-28343000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr10:28342400-28343000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:28342400-28343200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr10:28342400-28343400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr10:28342400-28344000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr10:28342400-28344200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:28342400-28344600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr10:28342400-28344600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr10:28342400-28345000	Enhancers	Hela-S3	cervix
33	chr10:28342400-28348400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr10:28342600-28342800	Enhancers	HMEC	breast
35	chr10:28342600-28342800	Enhancers	HSMMtube	muscle
36	chr10:28342600-28343200	Enhancers	NHLF	lung
37	chr10:28342600-28343400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:28342600-28344000	Enhancers	Rectal Smooth Muscle	rectum
39	chr10:28342600-28344200	Enhancers	HSMM	muscle
40	chr10:28342600-28344200	Enhancers	NH-A	brain
41	chr10:28342600-28344200	Enhancers	NHDF-Ad	bronchial
42	chr10:28342600-28344800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:28342600-28345000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr10:28342600-28350000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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