Variant report

Variant	rs13149938
Chromosome Location	chr4:87768517-87768518
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10015508	0.81[TSI][hapmap]
rs13106574	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13120839	0.89[ASW][hapmap];0.81[TSI][hapmap]
rs17012114	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17012130	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28495376	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28574613	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28682481	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34881728	0.91[EUR][1000 genomes]
rs35392566	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4639036	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58866123	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62305606	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6811350	0.89[ASW][hapmap];0.81[TSI][hapmap]
rs727143	0.81[TSI][hapmap]
rs72874293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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
rs13149938	PTPN13	cis	cerebellum	SCAN
rs13149938	AFF1	cis	lymphoblastoid	seeQTL
rs13149938	DMP1	cis	cerebellum	SCAN
rs13149938	AFF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87743200-87769400	Weak transcription	Right Ventricle	heart
2	chr4:87757200-87769200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:87763600-87769400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:87766200-87768800	Weak transcription	Esophagus	oesophagus
5	chr4:87767000-87771000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:87767200-87769000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:87767200-87769200	Weak transcription	Left Ventricle	heart
8	chr4:87767200-87769400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:87767200-87769400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:87767400-87768800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:87767400-87769600	Active TSS	NHEK	skin
12	chr4:87767600-87768800	Weak transcription	HMEC	breast
13	chr4:87767600-87769600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:87768000-87768600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:87768000-87769000	Active TSS	Adipose Nuclei	Adipose
16	chr4:87768000-87770800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:87768200-87768800	Active TSS	Right Atrium	heart
18	chr4:87768200-87769000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:87768200-87769000	Enhancers	NHDF-Ad	bronchial
20	chr4:87768200-87771400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:87768400-87769000	Enhancers	Osteobl	bone
22	chr4:87768400-87769200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:87768400-87769200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:87768400-87770200	Active TSS	Pancreatic Islets	Pancreatic Islet

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