Variant report

Variant	rs1580004
Chromosome Location	chr11:10370420-10370421
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1580005	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1580006	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2015148	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2084600	0.80[EUR][1000 genomes]
rs2923095	0.81[EUR][1000 genomes]
rs2923098	0.81[AFR][1000 genomes]
rs2957683	0.80[EUR][1000 genomes]
rs2957688	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2957689	0.81[AFR][1000 genomes]
rs2957691	0.81[AFR][1000 genomes]
rs61147745	0.81[EUR][1000 genomes]
rs7927363	0.81[AFR][1000 genomes]
rs7941414	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1580004	LYVE1	cis	parietal	SCAN
rs1580004	OR10A5	cis	cerebellum	SCAN
rs1580004	SYT9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10367400-10372000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:10368800-10373000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:10369600-10374200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:10369800-10371400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:10369800-10373000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:10369800-10373000	Enhancers	Adipose Nuclei	Adipose
7	chr11:10369800-10374000	Enhancers	HSMM	muscle
8	chr11:10369800-10374000	Enhancers	NHDF-Ad	bronchial
9	chr11:10369800-10374200	Enhancers	NHLF	lung
10	chr11:10369800-10378000	Enhancers	Placenta	Placenta
11	chr11:10370000-10372800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:10370000-10373000	Enhancers	HepG2	liver
13	chr11:10370000-10374200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr11:10370000-10374200	Enhancers	Osteobl	bone
15	chr11:10370200-10370800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:10370200-10370800	Enhancers	Fetal Heart	heart
17	chr11:10370200-10370800	Enhancers	Pancreas	Pancrea
18	chr11:10370200-10371600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:10370200-10372200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr11:10370200-10373200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:10370200-10373200	Enhancers	HSMMtube	muscle
22	chr11:10370200-10374200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:10370400-10371600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr11:10370400-10372400	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links