Variant report

Variant	rs9927594
Chromosome Location	chr16:79793766-79793767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:79793424..79795862-chr16:79801768..79804269,2	K562	blood:
2	chr16:79792741..79795517-chr16:79798638..79801342,2	K562	blood:
3	chr16:79793734..79796159-chr16:79809178..79810688,2	MCF-7	breast:
4	chr16:79792848..79795161-chr16:79799446..79800979,2	MCF-7	breast:
5	chr16:79785733..79789270-chr16:79790871..79794406,3	K562	blood:
6	chr16:79632870..79636122-chr16:79791499..79795376,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261390	Chromatin interaction
ENSG00000178573	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10871378	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs11150197	0.82[JPT][hapmap]
rs11860057	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12448881	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12716880	0.83[EUR][1000 genomes]
rs13334268	0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs13337701	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13337703	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13338008	0.87[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs13338235	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16951260	0.86[ASN][1000 genomes]
rs16951261	0.86[ASN][1000 genomes]
rs16951264	0.84[ASN][1000 genomes]
rs16951284	0.87[ASN][1000 genomes]
rs16951299	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs16951301	0.92[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs16951302	0.87[ASN][1000 genomes]
rs16951303	0.87[ASN][1000 genomes]
rs16951310	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs16951312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16951318	0.87[ASN][1000 genomes]
rs16951320	0.92[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs16951359	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28420623	0.87[ASN][1000 genomes]
rs28433357	0.87[ASN][1000 genomes]
rs28536718	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28691811	0.87[ASN][1000 genomes]
rs4257219	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs4296269	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4302049	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4319779	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4319782	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4322684	0.87[ASN][1000 genomes]
rs4327063	0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4372706	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4387616	0.86[JPT][hapmap]
rs4411509	0.92[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4435267	0.83[JPT][hapmap]
rs4470160	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4485383	0.83[JPT][hapmap]
rs4528586	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4547344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4567730	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4567731	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4603571	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4614737	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4632145	0.84[ASN][1000 genomes]
rs4632146	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4633733	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889024	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889026	0.94[CEU][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs56986701	0.84[ASN][1000 genomes]
rs59680118	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60153062	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62041321	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62041342	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62041343	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6564696	0.85[ASN][1000 genomes]
rs6564697	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6564698	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6564699	0.87[ASN][1000 genomes]
rs6564700	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs6564701	0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs6564702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6564703	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6564704	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67364537	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7187216	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7190102	0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7190298	0.92[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs7191995	0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7199398	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7200600	0.85[ASN][1000 genomes]
rs7200937	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7205712	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72810418	0.86[ASN][1000 genomes]
rs72810426	0.86[ASN][1000 genomes]
rs72810440	0.84[ASN][1000 genomes]
rs7499783	0.81[ASN][1000 genomes]
rs8045678	0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs8052982	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8053230	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8057083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8060038	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs8060072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8061610	0.87[ASN][1000 genomes]
rs8062324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8063650	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9673780	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9673947	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9921624	0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9922033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9923844	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9925997	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9926635	0.87[ASN][1000 genomes]
rs9927598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928163	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929497	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9931431	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9936175	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9936192	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9936261	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9939090	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9939565	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2755409	chr16:79776699-79816299	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9927594	CHST5	cis	parietal	SCAN
rs9927594	RP11-345M22.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79789000-79794000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr16:79789200-79801400	Weak transcription	Fetal Muscle Leg	muscle
3	chr16:79789200-79802000	Weak transcription	Primary T cells from cord blood	blood
4	chr16:79789400-79801400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr16:79791600-79793800	Weak transcription	K562	blood
6	chr16:79792000-79794000	Enhancers	HMEC	breast
7	chr16:79792600-79794000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr16:79792600-79794200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr16:79792800-79794200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr16:79792800-79794800	Weak transcription	Fetal Intestine Small	intestine
11	chr16:79792800-79801600	Weak transcription	Esophagus	oesophagus
12	chr16:79792800-79801800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr16:79792800-79804000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr16:79793200-79797200	Weak transcription	Fetal Lung	lung
15	chr16:79793200-79801200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr16:79793400-79794000	Weak transcription	Fetal Intestine Large	intestine
17	chr16:79793400-79801600	Weak transcription	NHEK	skin
18	chr16:79793400-79801800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr16:79793600-79801800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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