Variant report

Variant	rs985273
Chromosome Location	chr10:116335246-116335247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11196778	0.88[EUR][1000 genomes]
rs12413487	0.86[CEU][hapmap];0.99[EUR][1000 genomes]
rs2483535	0.81[TSI][hapmap]
rs2483538	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2483539	0.81[TSI][hapmap]
rs2483541	0.81[TSI][hapmap]
rs2483548	0.81[TSI][hapmap]
rs2483549	0.93[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2483553	0.81[TSI][hapmap]
rs2483560	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2483563	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483568	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483578	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483581	0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483590	0.88[EUR][1000 genomes]
rs2497663	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2497730	0.81[TSI][hapmap]
rs2497731	0.81[TSI][hapmap]
rs2497733	0.93[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2497740	0.85[TSI][hapmap]
rs2497743	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2497747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128920	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4998667	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58938015	0.99[EUR][1000 genomes]
rs60588618	0.88[EUR][1000 genomes]
rs72826986	0.88[EUR][1000 genomes]
rs72826987	0.88[EUR][1000 genomes]
rs72829115	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7913199	0.86[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7915301	0.82[AMR][1000 genomes]
rs9421186	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9421190	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116311600-116336600	Weak transcription	Colonic Mucosa	Colon
2	chr10:116318000-116337200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr10:116318400-116336600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr10:116321400-116336600	Weak transcription	Fetal Lung	lung
5	chr10:116323000-116336000	Weak transcription	Lung	lung
6	chr10:116323400-116352000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:116323800-116352000	Weak transcription	Fetal Intestine Large	intestine
8	chr10:116324200-116337400	Weak transcription	Fetal Stomach	stomach
9	chr10:116325400-116335600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr10:116325600-116336000	Weak transcription	Fetal Muscle Leg	muscle
11	chr10:116330400-116336000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr10:116331000-116339000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr10:116331400-116335400	Weak transcription	NHEK	skin
14	chr10:116331400-116336000	Weak transcription	Brain Anterior Caudate	brain
15	chr10:116331400-116336000	Weak transcription	Ovary	ovary
16	chr10:116331600-116335800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr10:116331800-116335400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:116331800-116335400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:116331800-116335400	Weak transcription	Aorta	Aorta
20	chr10:116331800-116336000	Weak transcription	NH-A	brain
21	chr10:116332200-116337000	Weak transcription	A549	lung
22	chr10:116333600-116336600	Weak transcription	Brain Substantia Nigra	brain
23	chr10:116333600-116345000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:116333800-116335400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr10:116334400-116335400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr10:116334400-116335400	Strong transcription	Fetal Intestine Small	intestine
27	chr10:116334600-116335400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:116334600-116335400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:116334600-116335400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:116334600-116335400	Genic enhancers	Liver	Liver
31	chr10:116334600-116335400	Strong transcription	Pancreatic Islets	Pancreatic Islet
32	chr10:116334600-116335400	Strong transcription	HSMMtube	muscle
33	chr10:116334600-116335600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr10:116334600-116335800	Enhancers	Esophagus	oesophagus
35	chr10:116334600-116337200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:116334800-116336600	Weak transcription	HUVEC	blood vessel
37	chr10:116335000-116335400	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr10:116335000-116335400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr10:116335000-116335400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr10:116335000-116335400	Active TSS	Stomach Smooth Muscle	stomach
41	chr10:116335000-116335800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr10:116335200-116335400	Transcr. at gene 5' and 3'	Right Ventricle	heart
43	chr10:116335200-116335600	Transcr. at gene 5' and 3'	Left Ventricle	heart
44	chr10:116335200-116335800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr10:116335200-116336000	Enhancers	Brain Cingulate Gyrus	brain
46	chr10:116335200-116336800	Enhancers	Pancreas	Pancrea
47	chr10:116335200-116336800	Enhancers	Psoas Muscle	Psoas
48	chr10:116335200-116337000	Enhancers	Brain Angular Gyrus	brain
49	chr10:116335200-116337000	Enhancers	Fetal Heart	heart
50	chr10:116335200-116337200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links