Variant report

Variant	rs11133243
Chromosome Location	chr4:53991306-53991307
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53987651..53991411-chr4:53993052..53996048,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10003612	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10008792	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10016471	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10028181	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11133244	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11936236	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17082398	0.83[JPT][hapmap]
rs28497299	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35275015	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3849654	0.83[JPT][hapmap]
rs4241973	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4616822	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864727	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66506011	0.81[ASN][1000 genomes]
rs71621063	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7378381	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9996126	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11133243	KIT	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53978800-54008000	Weak transcription	Primary T cells from cord blood	blood
2	chr4:53980400-53993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:53985600-53991400	Enhancers	HepG2	liver
4	chr4:53986200-53993000	Weak transcription	Fetal Stomach	stomach
5	chr4:53986200-53993200	Weak transcription	Fetal Kidney	kidney
6	chr4:53986200-53993600	Weak transcription	Psoas Muscle	Psoas
7	chr4:53986600-53993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:53986600-53994600	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:53986800-54010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:53986800-54011000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:53987600-53993600	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:53987800-53993600	Weak transcription	Aorta	Aorta
13	chr4:53987800-53993800	Weak transcription	Adipose Nuclei	Adipose
14	chr4:53987800-54016800	Weak transcription	NHLF	lung
15	chr4:53988000-53992800	Weak transcription	Ovary	ovary
16	chr4:53988000-53993800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:53988000-53994400	Weak transcription	NHDF-Ad	bronchial
18	chr4:53988000-53997600	Weak transcription	Osteobl	bone
19	chr4:53988200-54008000	Weak transcription	Primary B cells from cord blood	blood
20	chr4:53988400-53992600	Weak transcription	Lung	lung
21	chr4:53988600-54011000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:53988800-53993600	Weak transcription	Right Atrium	heart
23	chr4:53989200-54010200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:53989600-53992800	Weak transcription	Fetal Lung	lung
25	chr4:53989600-53995000	Weak transcription	Brain Substantia Nigra	brain
26	chr4:53990000-53991400	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:53990000-53993400	Weak transcription	Fetal Intestine Large	intestine
28	chr4:53990000-53995000	Weak transcription	HUVEC	blood vessel
29	chr4:53990400-53995000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links