Variant report

Variant	rs13232524
Chromosome Location	chr7:100512824-100512825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1054391	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11973000	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11978697	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12666785	0.92[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12669120	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs12672665	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12705094	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs12705097	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13225631	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13240020	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13241786	0.85[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs15624	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1799806	0.82[EUR][1000 genomes]
rs2405973	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2405974	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2405975	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571598	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28852509	0.87[EUR][1000 genomes]
rs2894713	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3087504	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs314369	0.84[EUR][1000 genomes]
rs314374	0.92[CEU][hapmap]
rs314375	0.96[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs314376	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs314377	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs314378	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs34005963	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757869	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3757870	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3757871	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3843541	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3843542	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3847063	0.92[CEU][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs3847064	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3847068	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3931823	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4727469	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4727470	0.95[ASN][1000 genomes]
rs4729615	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4729616	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs4729617	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4729618	0.94[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs4729619	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4729620	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6465776	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs6942607	0.92[CEU][hapmap]
rs6954151	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs6976053	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs7783457	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs7783543	0.89[EUR][1000 genomes]
rs7798613	0.86[EUR][1000 genomes]
rs7803865	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9718841	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13232524	PLOD3	cis	cerebellum	SCAN
rs13232524	ZNF3	cis	parietal	SCAN
rs13232524	TRIP6	cis	multi-tissue	Pritchard
rs13232524	C7orf59	cis	parietal	SCAN
rs13232524	EPHB4	cis	multi-tissue	Pritchard
rs13232524	LOC402682	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100504200-100516400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:100507800-100513800	Weak transcription	Colonic Mucosa	Colon
3	chr7:100508400-100514000	Weak transcription	K562	blood
4	chr7:100510400-100514000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:100510400-100514200	Weak transcription	Placenta	Placenta
6	chr7:100511000-100513000	Enhancers	Liver	Liver
7	chr7:100511000-100513000	Enhancers	Fetal Intestine Large	intestine
8	chr7:100511000-100513000	Enhancers	Stomach Mucosa	stomach
9	chr7:100511600-100513000	Enhancers	Pancreas	Pancrea
10	chr7:100512000-100513000	Enhancers	A549	lung
11	chr7:100512400-100514000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr7:100512600-100513000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:100512600-100513000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr7:100512600-100514000	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr7:100512600-100515800	Weak transcription	Fetal Intestine Small	intestine
16	chr7:100512800-100514000	Weak transcription	Duodenum Mucosa	Duodenum

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