Variant report

Variant	rs6839166
Chromosome Location	chr4:57739899-57739900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57739739..57741859-chr4:57787716..57790599,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10016108	1.00[CHB][hapmap]
rs11133472	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11573128	1.00[CHB][hapmap];0.92[MEX][hapmap]
rs11721387	0.82[ASN][1000 genomes]
rs11726410	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726443	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726548	0.82[ASN][1000 genomes]
rs11727329	1.00[ASN][1000 genomes]
rs11730321	0.89[CEU][hapmap];0.95[GIH][hapmap];0.90[TSI][hapmap]
rs11730396	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11731657	0.82[ASN][1000 genomes]
rs11732394	1.00[CHB][hapmap]
rs13123018	0.92[ASN][1000 genomes]
rs13125082	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs13128671	0.92[ASN][1000 genomes]
rs13130600	1.00[ASN][1000 genomes]
rs13130604	0.92[ASN][1000 genomes]
rs13146090	1.00[CHB][hapmap];0.85[MEX][hapmap]
rs13146153	1.00[CHB][hapmap]
rs1618761	1.00[CHB][hapmap]
rs17087358	1.00[CHB][hapmap]
rs17183291	1.00[CHB][hapmap]
rs2412761	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34308849	0.91[ASN][1000 genomes]
rs34840470	0.91[ASN][1000 genomes]
rs34937594	0.91[ASN][1000 genomes]
rs35185186	0.92[ASN][1000 genomes]
rs35318869	0.91[ASN][1000 genomes]
rs4109037	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs41495551	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap]
rs4413466	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443350	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56143151	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56309796	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62308068	0.82[ASN][1000 genomes]
rs62308099	0.91[ASN][1000 genomes]
rs62308100	0.91[ASN][1000 genomes]
rs62308107	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62308110	0.80[EUR][1000 genomes]
rs62308153	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66619445	0.92[ASN][1000 genomes]
rs6835102	0.80[EUR][1000 genomes]
rs6835108	0.80[EUR][1000 genomes]
rs6857005	0.81[EUR][1000 genomes]
rs6858216	0.80[EUR][1000 genomes]
rs7656865	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7684642	0.91[ASN][1000 genomes]
rs7685053	0.91[ASN][1000 genomes]
rs9055	0.92[ASN][1000 genomes]
rs9760540	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv822561	chr4:57736121-57747867	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6839166	WDR17	trans	cerebellum	SCAN
rs6839166	IGFBP7	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57727800-57740600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:57737200-57740800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr4:57738000-57740400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:57738000-57740600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:57738000-57740600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:57738000-57740600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:57738000-57740600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:57738000-57741400	Weak transcription	GM12878-XiMat	blood
9	chr4:57738000-57742800	Weak transcription	Spleen	Spleen
10	chr4:57738000-57744200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:57738200-57740400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:57738200-57740600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:57738200-57740600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:57738200-57746400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:57738600-57740400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:57738600-57740400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:57739200-57741200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:57739800-57740400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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