Variant report

Variant	rs17178078
Chromosome Location	chr4:73867915-73867916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1052080	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.85[ASN][1000 genomes]
rs11721329	0.85[ASN][1000 genomes]
rs11727957	0.83[ASN][1000 genomes]
rs11929937	0.85[ASN][1000 genomes]
rs11939939	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap]
rs12500051	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs12507846	0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs13107336	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs13135799	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13149759	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs13151642	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs34230856	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs34716955	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs3762883	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs62309635	0.85[ASN][1000 genomes]
rs67424539	0.83[ASN][1000 genomes]
rs6855349	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs7442235	0.85[ASN][1000 genomes]
rs7666763	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7690615	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs973541	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949371	chr4:73678470-74094500	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1005704	chr4:73708248-73907315	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv829971	chr4:73709753-73880451	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv432611	chr4:73740665-74099265	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv998707	chr4:73753922-74044843	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv537136	chr4:73753922-74044843	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv917017	chr4:73754127-74044830	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1013174	chr4:73785324-74031884	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv537137	chr4:73785324-74031884	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1012068	chr4:73817769-74003079	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv1014088	chr4:73817769-74031884	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv537138	chr4:73817769-74031884	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv533502	chr4:73819067-74044813	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17178078	COX18	cis	cerebellum	SCAN
rs17178078	CLVS2	trans	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73867600-73868000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:73867600-73868000	Enhancers	HUES6 Cell Line	embryonic stem cell

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