Variant report

Variant	rs7202977
Chromosome Location	chr16:76335822-76335823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11860370	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11866920	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12716805	1.00[ASN][1000 genomes]
rs12716806	1.00[ASN][1000 genomes]
rs12919539	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12919712	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12920627	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12924588	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12925117	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12926746	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs12928176	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12929147	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12929868	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12930031	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934879	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12935373	0.81[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935398	0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs13333703	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13339334	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428754	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428755	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428757	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1428758	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1428759	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428760	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477376	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1594027	1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1594028	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17562570	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17617031	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]
rs17648226	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1835074	0.91[ASN][1000 genomes]
rs2052866	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195430	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2216744	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28480106	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28529152	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28604279	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665922	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2866710	0.96[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866712	0.81[CEU][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs34041809	0.90[ASN][1000 genomes]
rs34952721	1.00[ASN][1000 genomes]
rs35330137	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35670143	0.90[ASN][1000 genomes]
rs35939460	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62049686	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62049687	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62049726	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62051169	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564315	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564320	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6564322	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66497322	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71378620	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71394257	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7185182	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187824	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[ASN][1000 genomes]
rs7188267	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7200703	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201435	0.92[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201761	1.00[ASN][1000 genomes]
rs747980	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747981	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044479	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044656	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046546	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055525	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8057110	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs929853	0.92[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9319493	0.85[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9673610	0.90[ASN][1000 genomes]
rs9673940	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9923380	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923941	0.82[CEU][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925921	1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9927237	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9927750	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939013	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944326	0.96[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944363	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription 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	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv833285	chr16:76136345-76345398	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7202977	CNTNAP4	cis	parietal	SCAN
rs7202977	BCAR1	cis	cerebellum	SCAN
rs7202977	CNTNAP4	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:76326600-76340600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr16:76327000-76336600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr16:76335800-76336000	Enhancers	Brain Hippocampus Middle	brain

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