Variant report

Variant	rs4729618
Chromosome Location	chr7:100501126-100501127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1054391	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10953305	0.83[ASN][1000 genomes]
rs11973000	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11978697	0.80[EUR][1000 genomes]
rs12666785	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12669120	0.96[CEU][hapmap];0.85[GIH][hapmap]
rs12672665	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12705094	0.96[CEU][hapmap];0.85[GIH][hapmap]
rs12705097	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13225631	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13232524	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13240020	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13241786	0.89[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs15624	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1799806	0.84[EUR][1000 genomes]
rs2405973	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2405974	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2405975	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2571598	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2720392	0.82[CHB][hapmap]
rs28852509	0.87[EUR][1000 genomes]
rs2894713	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3087504	0.96[CEU][hapmap];0.85[GIH][hapmap]
rs314369	0.86[EUR][1000 genomes]
rs314374	0.96[CEU][hapmap]
rs314375	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs314376	0.96[CEU][hapmap];0.85[GIH][hapmap]
rs314377	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs314378	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs34005963	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3757869	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3757870	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3757871	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3843541	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3843542	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3847063	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3847064	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3847068	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3931823	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4727469	0.96[CEU][hapmap]
rs4729615	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[EUR][1000 genomes]
rs4729616	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs4729617	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4729619	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4729620	0.96[CEU][hapmap]
rs6465776	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs6942607	0.96[CEU][hapmap]
rs6954151	0.96[CEU][hapmap];0.85[GIH][hapmap]
rs6976053	0.92[CEU][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap]
rs7783457	0.96[CEU][hapmap];0.85[GIH][hapmap]
rs7783543	0.91[EUR][1000 genomes]
rs7798613	0.87[EUR][1000 genomes]
rs7803865	0.96[CEU][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap]
rs9718841	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4729618	ZNF3	cis	parietal	SCAN
rs4729618	PLOD3	cis	cerebellum	SCAN
rs4729618	C7orf59	cis	parietal	SCAN
rs4729618	SHFM1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100498400-100501200	Enhancers	Fetal Intestine Large	intestine
2	chr7:100498400-100501200	Enhancers	Fetal Intestine Small	intestine
3	chr7:100498400-100501200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr7:100498800-100504000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:100499000-100504800	Weak transcription	Pancreas	Pancrea

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