Variant report

Variant	rs2483580
Chromosome Location	chr10:116347338-116347339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10885572	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10885573	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10885575	0.91[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs10885584	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11196779	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11196780	0.92[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11196781	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11196791	0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs12569428	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1413193	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1413194	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1413195	0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1537490	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1537491	0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1537492	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2145894	0.92[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2247528	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2247624	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2253338	0.81[TSI][hapmap]
rs2475242	0.82[EUR][1000 genomes]
rs2483531	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483564	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2483567	0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs2483571	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483577	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2483579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483584	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483585	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483586	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2483587	0.92[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483588	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483595	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483596	0.92[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483599	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483612	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2497656	0.83[AMR][1000 genomes]
rs2497658	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2497659	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2497662	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2497712	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2497717	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2497718	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2497719	0.92[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2497720	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2497721	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2497722	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2497723	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2901044	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[ASN][1000 genomes]
rs35078486	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4514325	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4568918	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56001223	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56086836	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs867736	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs883511	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs883768	0.92[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2483580	SHOC2	cis	parietal	SCAN
rs2483580	TECTB	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116323400-116352000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:116323800-116352000	Weak transcription	Fetal Intestine Large	intestine
3	chr10:116335400-116351600	Weak transcription	Fetal Intestine Small	intestine
4	chr10:116336800-116359800	Weak transcription	Lung	lung
5	chr10:116336800-116360000	Weak transcription	Fetal Muscle Leg	muscle
6	chr10:116337000-116360200	Weak transcription	Esophagus	oesophagus
7	chr10:116337400-116352800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr10:116337600-116353000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:116337800-116350000	Weak transcription	Liver	Liver
10	chr10:116337800-116362600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:116341400-116356800	Weak transcription	Brain Anterior Caudate	brain
12	chr10:116342200-116359800	Weak transcription	Adipose Nuclei	Adipose
13	chr10:116343800-116352000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:116345000-116349800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:116345000-116382400	Weak transcription	HSMM	muscle
16	chr10:116345800-116364000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr10:116346000-116352200	Weak transcription	HSMMtube	muscle
18	chr10:116346000-116352600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr10:116346000-116356000	Weak transcription	Right Atrium	heart
20	chr10:116346200-116347400	Weak transcription	Left Ventricle	heart
21	chr10:116346200-116347400	Weak transcription	Right Ventricle	heart
22	chr10:116346200-116360000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr10:116346400-116355200	Weak transcription	Fetal Heart	heart
24	chr10:116346600-116347800	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links