Variant report

Variant	rs7680588
Chromosome Location	chr4:86693753-86693754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10017047	0.93[CEU][hapmap]
rs10033273	0.93[CEU][hapmap]
rs1020584	1.00[CEU][hapmap]
rs11097072	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097073	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097074	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731040	0.82[MEX][hapmap]
rs11735639	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs12054628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12650494	0.82[MEX][hapmap]
rs13112493	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs13123125	0.98[ASN][1000 genomes]
rs13128115	0.93[CEU][hapmap];0.95[MEX][hapmap]
rs13146939	0.92[CEU][hapmap]
rs13152150	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs1482091	0.82[MEX][hapmap]
rs1482092	0.82[AMR][1000 genomes]
rs17010599	0.82[MEX][hapmap]
rs17010632	0.93[CEU][hapmap]
rs17010697	1.00[CEU][hapmap]
rs17010839	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1871864	0.93[CEU][hapmap]
rs1871865	0.93[CEU][hapmap]
rs343848	0.83[EUR][1000 genomes]
rs343852	0.83[EUR][1000 genomes]
rs41477846	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs4413396	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs56989679	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6819529	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6831420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855390	0.80[AMR][1000 genomes]
rs72656285	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72656294	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7439720	0.93[CEU][hapmap]
rs7674888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677064	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs7682971	0.82[MEX][hapmap]
rs931195	0.93[CEU][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879517	chr4:86677107-86739805	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7680588	HERC5	cis	cerebellum	SCAN
rs7680588	PKD2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86663400-86699800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:86676800-86697800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:86682000-86697000	Weak transcription	Psoas Muscle	Psoas
4	chr4:86683200-86699000	Weak transcription	Primary B cells from cord blood	blood
5	chr4:86683800-86695200	Weak transcription	HMEC	breast
6	chr4:86684600-86695800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr4:86684800-86695200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:86684800-86705600	Weak transcription	Small Intestine	intestine
9	chr4:86686200-86695000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:86688600-86694400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:86688600-86694400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:86688600-86694400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:86688600-86696800	Weak transcription	Fetal Kidney	kidney
14	chr4:86691000-86694400	Weak transcription	HUVEC	blood vessel
15	chr4:86692800-86693800	Weak transcription	Stomach Mucosa	stomach
16	chr4:86692800-86695000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:86693000-86694000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:86693200-86694600	Enhancers	NHDF-Ad	bronchial
19	chr4:86693400-86694000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:86693600-86694400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:86693600-86694800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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