Variant report

Variant	rs13139198
Chromosome Location	chr4:56049425-56049426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10012700	0.89[EUR][1000 genomes]
rs10014689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10017184	0.98[ASN][1000 genomes]
rs10019018	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030224	0.89[EUR][1000 genomes]
rs10213072	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11133365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723072	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12152606	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12504287	0.89[EUR][1000 genomes]
rs12509589	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716020	0.87[EUR][1000 genomes]
rs12716021	0.87[EUR][1000 genomes]
rs13107781	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115127	0.82[EUR][1000 genomes]
rs13128075	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13143119	0.82[EUR][1000 genomes]
rs13143543	0.82[EUR][1000 genomes]
rs13146373	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1380072	0.89[EUR][1000 genomes]
rs1380073	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551636	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551637	0.89[EUR][1000 genomes]
rs1551638	0.89[EUR][1000 genomes]
rs17081850	0.89[EUR][1000 genomes]
rs17081852	0.89[EUR][1000 genomes]
rs17081854	0.89[EUR][1000 genomes]
rs17081857	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870381	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870382	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993584	0.82[EUR][1000 genomes]
rs1993585	0.82[EUR][1000 genomes]
rs1993586	0.82[EUR][1000 genomes]
rs2015048	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085620	0.87[EUR][1000 genomes]
rs2085621	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125486	0.89[EUR][1000 genomes]
rs2125488	0.89[EUR][1000 genomes]
rs28702837	0.93[ASN][1000 genomes]
rs28841975	1.00[ASN][1000 genomes]
rs4241993	0.89[EUR][1000 genomes]
rs4277836	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4458511	0.89[EUR][1000 genomes]
rs4864961	0.89[EUR][1000 genomes]
rs4864963	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6554241	0.89[EUR][1000 genomes]
rs6554242	0.89[EUR][1000 genomes]
rs6821185	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs733378	0.89[EUR][1000 genomes]
rs7696873	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56036000-56050600	Weak transcription	Pancreas	Pancrea
2	chr4:56042400-56049800	Weak transcription	HSMM	muscle
3	chr4:56042600-56050600	Weak transcription	Placenta	Placenta
4	chr4:56042800-56050200	Weak transcription	Lung	lung
5	chr4:56042800-56050200	Weak transcription	Hela-S3	cervix
6	chr4:56044200-56050600	Weak transcription	Right Atrium	heart
7	chr4:56044600-56051200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:56046800-56054200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:56047600-56050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:56047800-56049800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:56047800-56050000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:56047800-56053800	Enhancers	HUVEC	blood vessel
13	chr4:56048000-56049600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:56048000-56049600	Weak transcription	NHLF	lung
15	chr4:56048000-56050200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:56048000-56050200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:56048000-56050400	Weak transcription	Aorta	Aorta
18	chr4:56048000-56050400	Weak transcription	HSMMtube	muscle
19	chr4:56048000-56050400	Enhancers	NH-A	brain
20	chr4:56048000-56050600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:56048000-56050600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:56048000-56050600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:56048000-56050600	Weak transcription	Fetal Lung	lung
24	chr4:56048000-56050600	Weak transcription	Left Ventricle	heart
25	chr4:56048000-56051200	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:56048200-56049600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:56048200-56050400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:56048200-56051000	Weak transcription	Fetal Heart	heart
29	chr4:56048400-56049600	Weak transcription	Osteobl	bone
30	chr4:56048400-56049800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:56048400-56050400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr4:56048800-56051000	Enhancers	NHDF-Ad	bronchial
33	chr4:56048800-56052000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:56048800-56052400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:56049000-56050000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:56049000-56050200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:56049000-56050600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:56049000-56052400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:56049200-56050200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:56049200-56050200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:56049200-56050400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr4:56049200-56052000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:56049200-56052200	Enhancers	HMEC	breast
44	chr4:56049200-56054200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr4:56049400-56050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:56049400-56051000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links