Variant report

Variant	rs7678571
Chromosome Location	chr4:87754713-87754714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10050311	0.85[JPT][hapmap]
rs6531935	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6820439	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6843070	0.80[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7678571	PTPN13	cis	cerebellum	SCAN
rs7678571	PTPN13	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87731200-87756000	Weak transcription	Pancreas	Pancrea
2	chr4:87732400-87760000	Weak transcription	Psoas Muscle	Psoas
3	chr4:87737800-87754800	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:87739800-87757600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:87740200-87755200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:87743200-87769400	Weak transcription	Right Ventricle	heart
7	chr4:87745400-87757400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:87752600-87764400	Weak transcription	Adipose Nuclei	Adipose
9	chr4:87752800-87755800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:87752800-87756200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:87753000-87755800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:87753000-87758000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:87753000-87765600	Weak transcription	Esophagus	oesophagus
14	chr4:87753000-87766800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:87753200-87755200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:87753200-87756200	Weak transcription	NHDF-Ad	bronchial
17	chr4:87753200-87757600	Enhancers	Hela-S3	cervix
18	chr4:87753200-87757800	Genic enhancers	NHEK	skin
19	chr4:87753200-87762000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:87753400-87758600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:87753600-87755000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:87753600-87756000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:87753600-87757200	Weak transcription	Left Ventricle	heart
24	chr4:87753800-87755000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:87754000-87755800	Weak transcription	HMEC	breast
26	chr4:87754400-87755800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:87754400-87756400	Enhancers	Fetal Lung	lung
28	chr4:87754400-87756600	Enhancers	NHLF	lung
29	chr4:87754600-87755600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:87754600-87755600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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