Variant report

Variant	rs13141097
Chromosome Location	chr4:87759069-87759070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10017360	0.84[ASN][1000 genomes]
rs10020861	0.85[TSI][hapmap]
rs11731586	0.84[ASN][1000 genomes]
rs11935015	0.84[ASN][1000 genomes]
rs11939730	0.84[ASN][1000 genomes]
rs12503661	0.84[ASN][1000 genomes]
rs13137142	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1374934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1550931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2594281	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs2594282	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2594284	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs2705622	0.84[ASN][1000 genomes]
rs2705623	0.88[ASN][1000 genomes]
rs2705624	0.88[ASN][1000 genomes]
rs2705627	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2922234	0.86[ASN][1000 genomes]
rs4508849	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4693788	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4693789	0.84[ASN][1000 genomes]
rs56414102	0.81[ASN][1000 genomes]
rs57477100	0.95[ASN][1000 genomes]
rs58275023	0.95[ASN][1000 genomes]
rs6531936	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6531937	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs73838351	0.95[ASN][1000 genomes]
rs7656537	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7657443	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7663218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8180256	0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs9654158	0.85[TSI][hapmap]

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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13141097	PTPN13	cis	parietal	SCAN
rs13141097	AFF1	cis	cerebellum	SCAN
rs13141097	PTPN13	cis	cerebellum	SCAN
rs13141097	COQ2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87732400-87760000	Weak transcription	Psoas Muscle	Psoas
2	chr4:87743200-87769400	Weak transcription	Right Ventricle	heart
3	chr4:87752600-87764400	Weak transcription	Adipose Nuclei	Adipose
4	chr4:87753000-87765600	Weak transcription	Esophagus	oesophagus
5	chr4:87753000-87766800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:87753200-87762000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:87756400-87759200	Weak transcription	HMEC	breast
8	chr4:87756400-87761800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:87756400-87762200	Weak transcription	NHDF-Ad	bronchial
10	chr4:87757200-87769200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:87758400-87759600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:87758600-87759600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:87758600-87759600	Enhancers	Fetal Brain Male	brain
14	chr4:87758600-87759600	Enhancers	Fetal Brain Female	brain
15	chr4:87758600-87759800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:87758600-87760400	Genic enhancers	NHEK	skin
17	chr4:87758800-87759400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:87758800-87759600	Enhancers	Colon Smooth Muscle	Colon
19	chr4:87758800-87759600	Enhancers	NHLF	lung
20	chr4:87758800-87761800	Enhancers	Fetal Lung	lung
21	chr4:87759000-87759600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:87759000-87768200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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