Variant report

Variant	rs2707575
Chromosome Location	chr7:147638723-147638724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10240221	0.86[CHB][hapmap]
rs11767010	0.96[CEU][hapmap]
rs11771941	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1574301	0.96[ASN][1000 genomes]
rs17237485	0.80[JPT][hapmap]
rs17237933	0.80[JPT][hapmap]
rs17432092	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17432209	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs1922889	0.90[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1997530	0.87[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs2141954	0.87[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs2178768	0.93[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs2178771	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2189883	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2204926	1.00[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2214682	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2527070	0.83[ASN][1000 genomes]
rs2707553	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2707576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707580	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707581	0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2707585	0.87[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs2708248	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2708261	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708284	0.96[CEU][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2708285	0.96[CEU][hapmap];0.93[GIH][hapmap]
rs2710074	0.84[ASN][1000 genomes]
rs2710075	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2710077	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2710082	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs2859687	0.89[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap]
rs4725758	0.86[CHB][hapmap]
rs6942912	0.86[CHB][hapmap]
rs6946207	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs6949561	0.86[CHB][hapmap]
rs6961407	0.96[CEU][hapmap]
rs6969904	0.86[CHB][hapmap]
rs73168529	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73168533	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7794874	0.80[JPT][hapmap]
rs8180832	0.92[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2707575	CNTNAP2	cis	cerebellum	SCAN
rs2707575	WDR86	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147638200-147638800	Enhancers	Aorta	Aorta
2	chr7:147638200-147639000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:147638200-147639200	Enhancers	Brain Anterior Caudate	brain
4	chr7:147638200-147639200	Enhancers	Brain Cingulate Gyrus	brain
5	chr7:147638200-147639200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:147638200-147639400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr7:147638400-147638800	Flanking Active TSS	Brain Substantia Nigra	brain
8	chr7:147638400-147639000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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