Variant report

Variant	rs17617031
Chromosome Location	chr16:76400985-76400986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11860370	0.84[CEU][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11866920	0.84[CEU][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12716805	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716806	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12919539	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12919712	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12920627	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12924588	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12925117	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12926746	0.83[EUR][1000 genomes]
rs12928176	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12929147	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12929868	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12930031	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934879	0.83[ASW][hapmap];0.89[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12935373	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935398	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13333703	0.85[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13339334	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428754	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428755	0.92[CEU][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428757	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1428758	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs1428759	0.81[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428760	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477376	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1594027	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1594028	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17562570	0.85[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17648226	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1835074	0.91[ASN][1000 genomes]
rs2052866	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195430	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2216744	0.81[CEU][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28480106	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28529152	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28604279	1.00[ASN][1000 genomes]
rs28665922	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2866710	0.81[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866712	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34041809	0.90[ASN][1000 genomes]
rs34952721	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35330137	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35670143	0.90[ASN][1000 genomes]
rs35939460	0.90[ASN][1000 genomes]
rs62049686	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62049687	1.00[ASN][1000 genomes]
rs62049726	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62051169	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564315	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564320	0.84[CEU][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6564322	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66497322	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71378620	1.00[ASN][1000 genomes]
rs71394257	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7185182	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187824	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7188267	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7200703	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201435	0.81[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201761	1.00[ASN][1000 genomes]
rs7202977	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747980	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747981	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044479	0.81[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044656	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046546	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055525	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8057110	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs929853	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs9319493	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9673610	0.90[ASN][1000 genomes]
rs9673940	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs9923380	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923941	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9925921	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9927237	0.90[ASN][1000 genomes]
rs9927750	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939013	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944326	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944363	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064607	chr16:75787129-76449101	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1065794	chr16:75792288-76434118	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv542961	chr16:75792288-76434118	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1059162	chr16:75929348-76730816	Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv572995	chr16:75935025-76708417	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv572996	chr16:75935025-76735249	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv817220	chr16:75939705-76735383	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1056021	chr16:75955522-76729765	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv542962	chr16:75955522-76729765	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv906935	chr16:76031737-76453110	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv906936	chr16:76031737-76768178	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv817549	chr16:76067068-76582099	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1065644	chr16:76166579-76475634	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv869200	chr16:76227867-76695732	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv833286	chr16:76243730-76444283	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	esv2763142	chr16:76271660-76461841	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv3425785	chr16:76398943-76402494	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17617031	CNTNAP4	cis	cerebellum	SCAN
rs17617031	CNTNAP4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:76390800-76406400	Weak transcription	Brain Angular Gyrus	brain
2	chr16:76394600-76409400	Weak transcription	Brain Hippocampus Middle	brain
3	chr16:76395400-76421800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr16:76399200-76401600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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