Variant report

Variant	rs10177513
Chromosome Location	chr2:190215527-190215528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10174225	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497699	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10755004	0.81[CEU][hapmap]
rs1157910	0.81[CEU][hapmap]
rs11677073	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11681937	0.83[ASN][1000 genomes]
rs11684417	0.83[ASN][1000 genomes]
rs11684869	1.00[CHB][hapmap]
rs11693810	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13010531	0.81[CEU][hapmap]
rs13032853	0.81[CEU][hapmap]
rs13406671	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1464136	0.84[EUR][1000 genomes]
rs1515873	0.83[ASN][1000 genomes]
rs1519182	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1519185	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1520857	0.81[CEU][hapmap]
rs1520862	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17198780	0.81[ASN][1000 genomes]
rs17198787	1.00[CHB][hapmap]
rs17270952	0.86[ASN][1000 genomes]
rs17270966	0.81[ASN][1000 genomes]
rs17271015	0.83[ASN][1000 genomes]
rs1996576	0.83[ASN][1000 genomes]
rs2680629	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683013	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2683014	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2683015	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683016	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28413975	0.81[EUR][1000 genomes]
rs4667281	0.81[CEU][hapmap]
rs55726777	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61528955	0.83[ASN][1000 genomes]
rs62182060	0.83[ASN][1000 genomes]
rs62182061	0.83[ASN][1000 genomes]
rs62182066	0.83[ASN][1000 genomes]
rs62182067	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182068	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62182069	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62182420	0.81[ASN][1000 genomes]
rs62183846	0.83[ASN][1000 genomes]
rs62183848	0.83[ASN][1000 genomes]
rs6434339	0.81[CEU][hapmap]
rs72912280	0.83[ASN][1000 genomes]
rs72912286	0.83[ASN][1000 genomes]
rs72914135	0.82[EUR][1000 genomes]
rs72914141	0.83[ASN][1000 genomes]
rs7564429	0.83[ASN][1000 genomes]
rs7576165	0.81[CEU][hapmap]
rs7577872	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963738	0.81[CEU][hapmap]
rs9808245	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875614	chr2:190110841-190254758	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10177513	COL5A2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190213600-190215600	Weak transcription	HSMMtube	muscle
2	chr2:190214600-190216000	Enhancers	Rectal Smooth Muscle	rectum
3	chr2:190214600-190216200	Enhancers	NHDF-Ad	bronchial
4	chr2:190214600-190216400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr2:190214800-190216400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:190215000-190216000	Enhancers	NH-A	brain
7	chr2:190215000-190216200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:190215000-190216200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:190215200-190215600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:190215200-190215600	Enhancers	Fetal Lung	lung
11	chr2:190215200-190215600	Enhancers	Fetal Stomach	stomach
12	chr2:190215200-190215800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:190215200-190215800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:190215200-190215800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:190215200-190215800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:190215200-190215800	Enhancers	Adipose Nuclei	Adipose
17	chr2:190215200-190216000	Enhancers	Colon Smooth Muscle	Colon
18	chr2:190215200-190216000	Enhancers	Ovary	ovary
19	chr2:190215200-190216000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr2:190215200-190216000	Enhancers	HUVEC	blood vessel
21	chr2:190215200-190216200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:190215200-190216200	Enhancers	HSMM	muscle
23	chr2:190215200-190216200	Enhancers	NHLF	lung
24	chr2:190215200-190216200	Enhancers	Osteobl	bone
25	chr2:190215400-190215600	Enhancers	HMEC	breast
26	chr2:190215400-190216000	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links