Variant report

Variant	rs7653164
Chromosome Location	chr3:143550855-143550856
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10513218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1394398	1.00[CHB][hapmap]
rs1504603	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1504604	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1504605	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16834862	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16854543	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1995529	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap]
rs1995530	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap]
rs2011297	1.00[CHB][hapmap]
rs2011303	1.00[CHB][hapmap]
rs2361205	0.81[ASN][1000 genomes]
rs2885195	1.00[CHB][hapmap]
rs4499594	1.00[CHB][hapmap]
rs56124843	1.00[ASN][1000 genomes]
rs57262535	1.00[ASN][1000 genomes]
rs58621433	1.00[ASN][1000 genomes]
rs59306133	0.89[AFR][1000 genomes]
rs59653678	1.00[ASN][1000 genomes]
rs60249173	0.81[ASN][1000 genomes]
rs60550983	0.81[ASN][1000 genomes]
rs6762196	1.00[ASN][1000 genomes]
rs6768399	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6780027	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap]
rs6794907	1.00[CHB][hapmap]
rs73869037	0.81[ASN][1000 genomes]
rs73869039	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73869041	0.81[ASN][1000 genomes]
rs73869049	0.86[AFR][1000 genomes]
rs7434217	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7613146	1.00[CHB][hapmap]
rs7624170	1.00[GIH][hapmap]
rs7637640	0.81[ASN][1000 genomes]
rs9289669	1.00[GIH][hapmap]
rs9824974	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs9847107	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7653164	CHST2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143539800-143558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:143541000-143554200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:143541400-143565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:143542000-143553600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:143542200-143552400	Weak transcription	Brain Angular Gyrus	brain
6	chr3:143542200-143553600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:143543600-143551400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:143544200-143552800	Weak transcription	Fetal Lung	lung
9	chr3:143545400-143558800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:143545600-143565400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:143545800-143551000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:143546000-143559000	Weak transcription	Primary B cells from cord blood	blood
13	chr3:143547000-143558200	Weak transcription	Esophagus	oesophagus
14	chr3:143548800-143551600	Enhancers	Stomach Mucosa	stomach
15	chr3:143548800-143551600	Enhancers	NHLF	lung
16	chr3:143548800-143551800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:143548800-143551800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:143549000-143551000	Enhancers	HUVEC	blood vessel
19	chr3:143549000-143551800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:143549000-143551800	Enhancers	HMEC	breast
21	chr3:143549000-143552800	Enhancers	Colon Smooth Muscle	Colon
22	chr3:143549200-143551000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:143549200-143565200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:143549400-143552400	Weak transcription	Aorta	Aorta
25	chr3:143549400-143565000	Weak transcription	Primary T cells from cord blood	blood
26	chr3:143549800-143551800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:143549800-143551800	Enhancers	Brain Substantia Nigra	brain
28	chr3:143549800-143552000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:143550000-143551200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:143550000-143551800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:143550000-143552000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:143550000-143558200	Weak transcription	Right Atrium	heart
33	chr3:143550000-143565200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:143550200-143551000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:143550200-143551200	Enhancers	Duodenum Mucosa	Duodenum
36	chr3:143550200-143558800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:143550400-143551000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:143550400-143551000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:143550400-143551200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr3:143550400-143551400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr3:143550400-143551800	Enhancers	NHDF-Ad	bronchial
42	chr3:143550400-143551800	Enhancers	NHEK	skin
43	chr3:143550400-143552400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:143550400-143552400	Weak transcription	Ovary	ovary
45	chr3:143550600-143551200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr3:143550600-143551200	Weak transcription	Adipose Nuclei	Adipose
47	chr3:143550600-143551400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:143550600-143551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:143550600-143551800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:143550600-143551800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links