Variant report

Variant	rs4794058
Chromosome Location	chr17:45597098-45597099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10048173	0.81[EUR][1000 genomes]
rs11079774	0.81[CEU][hapmap]
rs11079783	0.86[ASW][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap]
rs11079784	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs11870935	0.89[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap]
rs11871606	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs12051716	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12103836	0.81[EUR][1000 genomes]
rs12452315	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs12943464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1962307	0.81[TSI][hapmap]
rs2317826	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs35159316	0.81[ASN][1000 genomes]
rs35794672	0.80[EUR][1000 genomes]
rs3760370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs3760371	0.86[ASW][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap]
rs3809868	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap]
rs4239162	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs4239163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4289035	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4793842	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs4793978	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs4794001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs4794007	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4794047	0.82[TSI][hapmap]
rs4794048	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs4794051	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62073965	0.81[EUR][1000 genomes]
rs62073966	0.92[EUR][1000 genomes]
rs62076549	0.83[ASN][1000 genomes]
rs6503796	0.81[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs6504872	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs7206971	0.92[CEU][hapmap]
rs7210738	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap]
rs7214799	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[TSI][hapmap]
rs7221548	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7222225	0.86[ASW][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap]
rs7222851	0.81[EUR][1000 genomes]
rs72829689	0.95[ASN][1000 genomes]
rs7350906	0.85[EUR][1000 genomes]
rs8065669	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs8065990	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8067286	0.90[EUR][1000 genomes]
rs8070463	0.85[CEU][hapmap];0.84[CHD][hapmap]
rs8072100	0.92[CEU][hapmap]
rs8072644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs8074149	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8075411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs8078686	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs8078880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9635762	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9911944	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv516872	chr17:45419139-45702280	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv525267	chr17:45451894-45735706	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1806110	chr17:45477544-45673592	Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv833468	chr17:45511563-45683164	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv469573	chr17:45511582-45698942	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv471701	chr17:45511583-45698942	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1793478	chr17:45518444-45671051	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv908569	chr17:45537395-45603094	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv1808961	chr17:45542951-45664746	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	esv33689	chr17:45551959-45664575	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv471513	chr17:45552080-45671439	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
18	nsv978433	chr17:45560111-45600707	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	nsv908570	chr17:45571502-45684651	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	esv1818529	chr17:45583088-45683095	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
21	nsv9567	chr17:45596159-45598008	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4794058	VPS25	cis	cerebellum	SCAN
rs4794058	TBKBP1	cis	lymphoblastoid	seeQTL
rs4794058	TBKBP1	cis	Nerve Tibial	GTEx
rs4794058	NPEPPS	cis	parietal	SCAN
rs4794058	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs4794058	DBF4B	cis	cerebellum	SCAN
rs4794058	SCRN2	cis	lung	GTEx
rs4794058	C17orf57	cis	parietal	SCAN
rs4794058	RAB5C	cis	parietal	SCAN
rs4794058	MRPL45P2	cis	lymphoblastoid	seeQTL
rs4794058	CDK5RAP3	cis	cerebellum	SCAN
rs4794058	MRPL45P2	cis	Muscle Skeletal	GTEx
rs4794058	C17orf57	cis	cerebellum	SCAN
rs4794058	TBKBP1	cis	Artery Tibial	GTEx
rs4794058	C17orf65	cis	cerebellum	SCAN
rs4794058	VPS25	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45596000-45597200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr17:45596400-45597800	Enhancers	K562	blood
3	chr17:45596600-45598200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr17:45596800-45597200	Weak transcription	A549	lung

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