Variant report

Variant	rs16872495
Chromosome Location	chr7:107992232-107992233
allele	A/C
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 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	chr7:107980565..107981546-chr7:107992150..107992675,2	MCF-7	breast:
4	chr7:107840521..107844716-chr7:107989632..107993969,4	MCF-7	breast:
5	chr7:107842032..107842538-chr7:107991881..107992471,2	MCF-7	breast:
6	chr7:107984388..107993798-chr7:108093279..108099270,17	MCF-7	breast:
7	chr7:107979669..107981682-chr7:107989556..107992605,3	MCF-7	breast:
8	chr7:107991286..107993466-chr7:108009431..108011060,2	MCF-7	breast:
9	chr7:107985603..107987833-chr7:107991095..107992631,2	K562	blood:
10	chr7:107938640..107940703-chr7:107991452..107994655,4	MCF-7	breast:
11	chr7:107843916..107845660-chr7:107990160..107992997,2	MCF-7	breast:
12	chr7:107991896..107993618-chr7:108006610..108008809,2	MCF-7	breast:
13	chr7:107975728..107977944-chr7:107990404..107993160,3	MCF-7	breast:
14	chr7:107936793..107941797-chr7:107984945..107993863,13	MCF-7	breast:
15	chr7:107942489..107944255-chr7:107991552..107993879,2	MCF-7	breast:
16	chr7:107991147..107992916-chr7:108051189..108054156,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1016148	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10487850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10953568	0.88[EUR][1000 genomes]
rs11763042	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11769966	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12538050	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12539530	0.83[MEX][hapmap]
rs12673082	0.86[CEU][hapmap];0.85[GIH][hapmap]
rs12673676	0.88[CEU][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12705448	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13221333	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13230316	0.82[MEX][hapmap]
rs13242951	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13243381	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13244715	0.82[MEX][hapmap]
rs17155485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17155518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17155522	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2098419	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300024	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300030	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34025892	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4142283	0.94[CEU][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4727703	0.94[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6956163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6975557	0.83[MEX][hapmap]
rs7778203	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7804045	0.83[MEX][hapmap]
rs969708	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.85[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
rs16872495	DNAJB9	cis	parietal	SCAN
rs16872495	RNF133	trans	parietal	SCAN

Chromatin state (count:14 , 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	chr7:107988200-107992600	Enhancers	A549	lung
4	chr7:107988800-107994200	Weak transcription	Pancreas	Pancrea
5	chr7:107989200-107997800	Weak transcription	Placenta	Placenta
6	chr7:107989800-107992400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:107989800-107999000	Weak transcription	HMEC	breast
8	chr7:107991600-107992600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr7:107991600-107993400	Enhancers	HepG2	liver
10	chr7:107991800-107992800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:107991800-107992800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:107991800-107993000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr7:107992000-107992600	Enhancers	HUVEC	blood vessel
14	chr7:107992000-107993800	Enhancers	Pancreatic Islets	Pancreatic Islet

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