Variant report

Variant	rs11719102
Chromosome Location	chr3:156786544-156786545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1032041	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1032044	0.88[JPT][hapmap]
rs10936054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10936055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10936058	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11715321	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11720579	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12636394	0.89[ASN][1000 genomes]
rs12636741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12638952	0.86[ASN][1000 genomes]
rs13082176	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1384541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1482854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1482855	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1482856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1482857	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1482859	0.91[ASN][1000 genomes]
rs1482866	0.85[ASN][1000 genomes]
rs1600978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1842840	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2046269	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2046270	0.89[ASN][1000 genomes]
rs2046273	0.84[AMR][1000 genomes]
rs2128535	0.80[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2220051	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28564228	0.89[ASN][1000 genomes]
rs35354535	0.89[ASN][1000 genomes]
rs35626159	0.88[ASN][1000 genomes]
rs4263246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4680332	1.00[JPT][hapmap]
rs4680337	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs6797982	0.81[EUR][1000 genomes]
rs6799034	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7612970	0.88[JPT][hapmap]
rs7616314	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7624328	0.88[JPT][hapmap]
rs7626027	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7637445	0.89[ASN][1000 genomes]
rs922864	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs931245	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs931246	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9790244	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9811993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9812759	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9818123	0.86[ASN][1000 genomes]
rs9818500	0.91[ASN][1000 genomes]
rs9818874	0.89[ASN][1000 genomes]
rs9829685	0.82[JPT][hapmap]
rs9859727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9867766	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][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	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11719102	LINC00886	cis	lung	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156782000-156787200	Enhancers	Fetal Thymus	thymus
2	chr3:156782400-156787600	Weak transcription	Stomach Mucosa	stomach
3	chr3:156782400-156794000	Weak transcription	Right Atrium	heart
4	chr3:156782600-156795000	Weak transcription	Fetal Heart	heart
5	chr3:156782800-156787600	Weak transcription	Fetal Intestine Large	intestine
6	chr3:156782800-156789400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:156782800-156795000	Weak transcription	Adipose Nuclei	Adipose
8	chr3:156783200-156786600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:156783200-156786600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:156783200-156786800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:156783400-156788200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:156783400-156793400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:156784000-156786600	Enhancers	Thymus	Thymus
14	chr3:156784400-156788600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:156784800-156787600	Weak transcription	Liver	Liver
16	chr3:156785000-156788000	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:156785000-156788400	Weak transcription	Brain Anterior Caudate	brain
18	chr3:156785200-156787800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:156785200-156787800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:156785200-156788200	Weak transcription	HSMM	muscle
21	chr3:156785200-156788400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:156785200-156791400	Weak transcription	NHLF	lung
23	chr3:156785200-156791600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:156785200-156791600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:156785200-156791600	Weak transcription	Brain Substantia Nigra	brain
26	chr3:156785200-156793400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:156785400-156786800	Weak transcription	Brain Angular Gyrus	brain
28	chr3:156785400-156787800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:156785400-156787800	Weak transcription	Osteobl	bone
30	chr3:156785400-156788400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:156785400-156788600	Weak transcription	NHDF-Ad	bronchial
32	chr3:156785400-156789600	Weak transcription	GM12878-XiMat	blood
33	chr3:156785600-156787800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:156786000-156791600	Weak transcription	NH-A	brain
35	chr3:156786200-156788000	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links