Variant report

Variant	rs10516757
Chromosome Location	chr4:86704797-86704798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12710823	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13120732	0.94[ASN][1000 genomes]
rs17010957	0.93[JPT][hapmap]
rs17393306	1.00[ASW][hapmap]
rs2014912	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6829822	0.92[ASN][1000 genomes]
rs7671129	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7687906	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7687940	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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 miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879517	chr4:86677107-86739805	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3465621	chr4:86704703-86707567	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3465618	chr4:86704769-86707507	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3465622	chr4:86704769-86707507	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10516757	THAP9	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86684800-86705600	Weak transcription	Small Intestine	intestine
2	chr4:86695400-86708200	Weak transcription	Pancreas	Pancrea
3	chr4:86697200-86707800	Weak transcription	Spleen	Spleen
4	chr4:86698000-86704800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:86700200-86705000	Weak transcription	Liver	Liver
6	chr4:86700600-86706800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:86701000-86704800	Weak transcription	Ovary	ovary
8	chr4:86701000-86705200	Weak transcription	Psoas Muscle	Psoas
9	chr4:86701000-86708000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:86701000-86708000	Weak transcription	HMEC	breast
11	chr4:86701000-86728800	Weak transcription	Right Ventricle	heart
12	chr4:86701200-86705000	Weak transcription	Fetal Stomach	stomach
13	chr4:86701200-86708800	Weak transcription	Right Atrium	heart
14	chr4:86701200-86715600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:86701800-86708800	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:86702200-86705200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:86702200-86705600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:86702200-86709800	Weak transcription	Fetal Kidney	kidney
19	chr4:86702200-86711200	Weak transcription	Fetal Lung	lung
20	chr4:86702400-86704800	Weak transcription	Adipose Nuclei	Adipose
21	chr4:86702400-86704800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:86702400-86704800	Weak transcription	HSMMtube	muscle
23	chr4:86702400-86707000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:86702800-86705000	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:86703000-86705000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr4:86703000-86705200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:86703000-86705400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:86703200-86705000	Weak transcription	Left Ventricle	heart
29	chr4:86703600-86706000	Enhancers	Rectal Smooth Muscle	rectum
30	chr4:86703800-86705000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:86703800-86705800	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr4:86704000-86715600	Enhancers	Osteobl	bone
33	chr4:86704000-86719800	Enhancers	NHDF-Ad	bronchial
34	chr4:86704200-86705000	Enhancers	Primary B cells from cord blood	blood
35	chr4:86704200-86705800	Flanking Active TSS	HUVEC	blood vessel
36	chr4:86704200-86706400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:86704200-86706400	Enhancers	HSMM	muscle
38	chr4:86704400-86704800	Weak transcription	NH-A	brain
39	chr4:86704400-86705600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:86704400-86709800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:86704400-86710000	Enhancers	NHLF	lung
42	chr4:86704600-86705000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr4:86704600-86705200	Active TSS	Aorta	Aorta
44	chr4:86704600-86705600	Enhancers	A549	lung
45	chr4:86704600-86706400	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links