Variant report

Variant	rs13230316
Chromosome Location	chr7:107991567-107991568
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:107988114..107994277-chr7:108093987..108097676,13	MCF-7	breast:
2	chr7:107885764..107888071-chr7:107990459..107993788,3	MCF-7	breast:
3	chr7:107840521..107844716-chr7:107989632..107993969,4	MCF-7	breast:
4	chr7:107984388..107993798-chr7:108093279..108099270,17	MCF-7	breast:
5	chr7:107979669..107981682-chr7:107989556..107992605,3	MCF-7	breast:
6	chr7:107991286..107993466-chr7:108009431..108011060,2	MCF-7	breast:
7	chr7:107985603..107987833-chr7:107991095..107992631,2	K562	blood:
8	chr7:107938640..107940703-chr7:107991452..107994655,4	MCF-7	breast:
9	chr7:107843916..107845660-chr7:107990160..107992997,2	MCF-7	breast:
10	chr7:107975728..107977944-chr7:107990404..107993160,3	MCF-7	breast:
11	chr7:107936793..107941797-chr7:107984945..107993863,13	MCF-7	breast:
12	chr7:107942489..107944255-chr7:107991552..107993879,2	MCF-7	breast:
13	chr7:107991147..107992916-chr7:108051189..108054156,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1016149	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12531089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12539530	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12539964	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs13242951	0.82[MEX][hapmap]
rs13244715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16872495	0.82[MEX][hapmap]
rs17155518	0.82[MEX][hapmap]
rs1990712	0.81[EUR][1000 genomes]
rs2080489	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2216259	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs2284285	0.81[JPT][hapmap]
rs2284286	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300027	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2395961	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs2395962	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs34294071	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34427132	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35669142	0.86[EUR][1000 genomes]
rs36063908	0.86[EUR][1000 genomes]
rs56102707	0.83[EUR][1000 genomes]
rs6948554	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957056	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6975557	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1019059	chr7:107935905-107995523	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1021783	chr7:107935905-107998281	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv2761354	chr7:107935905-107998293	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv1031824	chr7:107935905-108006038	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1017288	chr7:107939739-108000837	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13230316	OAT	trans	lymphoblastoid	seeQTL
rs13230316	LRRN3	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107986600-107998200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:107988000-108001000	Weak transcription	HSMMtube	muscle
3	chr7:107988200-107991600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr7:107988200-107992600	Enhancers	A549	lung
5	chr7:107988800-107994200	Weak transcription	Pancreas	Pancrea
6	chr7:107989200-107997800	Weak transcription	Placenta	Placenta
7	chr7:107989600-107991800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:107989800-107991800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr7:107989800-107992400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:107989800-107999000	Weak transcription	HMEC	breast
11	chr7:107990400-107991800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links