Variant report

Variant	rs4566193
Chromosome Location	chr16:76552841-76552842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12051273	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12596018	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2008006	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2135621	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28526498	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34036659	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4270198	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4334321	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4485401	0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4490031	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4506930	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4573954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62048239	0.80[ASN][1000 genomes]
rs6564346	1.00[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6564350	0.86[JPT][hapmap]
rs71394267	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7186892	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7188191	0.81[ASN][1000 genomes]
rs7204321	0.87[EUR][1000 genomes]
rs8062846	0.86[JPT][hapmap]
rs950530	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9927836	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9928928	0.84[JPT][hapmap]
rs9938136	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv906943	chr16:76413757-76768178	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1063069	chr16:76462850-77214064	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
12	nsv542963	chr16:76462850-77214064	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
13	nsv833287	chr16:76482823-76666426	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv1883	chr16:76519215-76563112	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv906944	chr16:76521236-76768178	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv529621	chr16:76521425-76769398	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	esv1821336	chr16:76540062-76554487	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv573047	chr16:76540798-76881625	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	esv2422474	chr16:76544108-77125562	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
20	nsv906945	chr16:76547629-76612750	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4566193	CNTNAP4	cis	Frontal Cortex	GTEx
rs4566193	CNTNAP4	cis	Temporal Cortex	GTEx
rs4566193	CNTNAP4	cis	Cerebellum	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:76525200-76554000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr16:76548200-76553000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:76551800-76553000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:76552200-76554400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr16:76552400-76553000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr16:76552400-76554200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr16:76552600-76553000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr16:76552600-76553000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:76552600-76554000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr16:76552600-76554400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr16:76552800-76553200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr16:76552800-76553800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr16:76552800-76554600	Enhancers	Brain Cingulate Gyrus	brain

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