Variant report

Variant	rs2275928
Chromosome Location	chr10:5147909-5147910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10160019	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10752003	0.85[ASN][1000 genomes]
rs10795250	0.86[ASN][1000 genomes]
rs10904429	0.86[ASN][1000 genomes]
rs10904430	0.87[ASN][1000 genomes]
rs11252940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11252942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11252943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11252944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11252945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11252946	0.98[ASN][1000 genomes]
rs11252947	0.97[ASN][1000 genomes]
rs11252948	0.98[ASN][1000 genomes]
rs11252949	0.98[ASN][1000 genomes]
rs11252950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11252951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11252961	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11252985	0.87[ASN][1000 genomes]
rs11253009	0.87[ASN][1000 genomes]
rs11499158	0.87[ASN][1000 genomes]
rs11499183	0.90[ASN][1000 genomes]
rs11499185	0.87[ASN][1000 genomes]
rs12242350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12244584	0.98[ASN][1000 genomes]
rs12244591	0.98[ASN][1000 genomes]
rs12255333	0.87[ASN][1000 genomes]
rs12259827	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12263243	0.93[ASN][1000 genomes]
rs12264305	0.87[ASN][1000 genomes]
rs12769666	0.98[ASN][1000 genomes]
rs12775913	0.94[ASN][1000 genomes]
rs12775922	0.97[ASN][1000 genomes]
rs12775924	0.95[ASN][1000 genomes]
rs12782982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17155732	1.00[ASN][1000 genomes]
rs17173403	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1892405	0.86[ASN][1000 genomes]
rs1937913	0.86[ASN][1000 genomes]
rs1937920	0.87[ASN][1000 genomes]
rs1937921	0.86[ASN][1000 genomes]
rs1937924	0.86[ASN][1000 genomes]
rs2154306	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2154307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2186172	0.87[ASN][1000 genomes]
rs2186173	0.87[ASN][1000 genomes]
rs2186174	0.88[ASN][1000 genomes]
rs2245191	0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs2398202	0.87[ASN][1000 genomes]
rs2398203	0.88[ASN][1000 genomes]
rs3209896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34277279	0.93[ASN][1000 genomes]
rs4347280	0.97[ASN][1000 genomes]
rs4414120	0.86[ASN][1000 genomes]
rs4636560	0.86[ASN][1000 genomes]
rs4880709	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs4881402	0.87[ASN][1000 genomes]
rs60725680	0.87[ASN][1000 genomes]
rs6601906	0.89[ASN][1000 genomes]
rs7068685	0.87[ASN][1000 genomes]
rs7070041	0.88[ASN][1000 genomes]
rs7086771	0.93[CHB][hapmap];0.97[CHD][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs7088288	0.86[ASN][1000 genomes]
rs7904863	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7921327	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9329316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9888062	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv1036566	chr10:5037926-5261426	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv549883	chr10:5037926-5275762	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv1047484	chr10:5076258-5261482	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv1036291	chr10:5076258-5456234	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv1042487	chr10:5090313-5196900	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv540463	chr10:5090313-5196900	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv540464	chr10:5108345-5196815	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv540465	chr10:5108345-5261482	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv540466	chr10:5114577-5196815	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv540467	chr10:5114577-5225365	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv540468	chr10:5114577-5261482	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv540469	chr10:5120774-5225365	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv540470	chr10:5120774-5261482	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
27	nsv540471	chr10:5133561-5261482	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
28	nsv540472	chr10:5133561-5284334	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
29	nsv466714	chr10:5142855-5175450	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
30	nsv549885	chr10:5142855-5175450	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2275928	AKR1C3	cis	cerebellum	SCAN
rs2275928	CALML5	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5137200-5149800	Weak transcription	Small Intestine	intestine
2	chr10:5137400-5149400	Weak transcription	HSMM	muscle
3	chr10:5137400-5149600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr10:5137400-5149600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:5137400-5149800	Weak transcription	Pancreas	Pancrea
6	chr10:5137400-5151600	Weak transcription	Brain Angular Gyrus	brain
7	chr10:5137400-5151800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:5137400-5152000	Weak transcription	Right Ventricle	heart
9	chr10:5137800-5150800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr10:5138200-5148400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr10:5138200-5151000	Weak transcription	Osteobl	bone
12	chr10:5138200-5151800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr10:5138600-5149200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:5138600-5149800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr10:5138600-5150200	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:5138600-5151800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr10:5138800-5151800	Weak transcription	Brain Anterior Caudate	brain
18	chr10:5138800-5151800	Weak transcription	Colonic Mucosa	Colon
19	chr10:5138800-5152000	Weak transcription	Psoas Muscle	Psoas
20	chr10:5139000-5151600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr10:5140000-5148200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:5140200-5148200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:5140200-5150400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr10:5140800-5148600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:5140800-5149800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:5142200-5148000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:5144400-5148000	Weak transcription	NHDF-Ad	bronchial
28	chr10:5145200-5151400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr10:5145600-5148400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:5145600-5148600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:5146000-5148000	Weak transcription	Gastric	stomach
32	chr10:5146000-5148000	Weak transcription	HSMMtube	muscle
33	chr10:5146000-5149600	Weak transcription	Thymus	Thymus
34	chr10:5146000-5150000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:5146000-5150400	Weak transcription	Fetal Intestine Small	intestine
36	chr10:5146000-5151600	Weak transcription	Hela-S3	cervix
37	chr10:5146000-5151800	Weak transcription	Esophagus	oesophagus
38	chr10:5146000-5157600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr10:5146200-5148000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr10:5147400-5148600	Genic enhancers	Liver	Liver
41	chr10:5147400-5150200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr10:5147400-5150200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr10:5147600-5148200	Genic enhancers	HepG2	liver
44	chr10:5147600-5148400	Genic enhancers	Adipose Nuclei	Adipose
45	chr10:5147800-5148000	Strong transcription	Left Ventricle	heart
46	chr10:5147800-5148200	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr10:5147800-5148400	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr10:5147800-5148400	Strong transcription	Lung	lung
49	chr10:5147800-5148400	Strong transcription	Ovary	ovary
50	chr10:5147800-5148400	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links