Variant report

Variant	rs2139596
Chromosome Location	chr14:72822644-72822645
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10136263	0.94[CHD][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10141305	0.89[ASN][1000 genomes]
rs10149207	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1072165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11620677	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs1356842	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1402063	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs1402064	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1996661	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs2190509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222311	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs2238195	0.83[CEU][hapmap]
rs2238207	0.80[TSI][hapmap]
rs2239246	0.88[CEU][hapmap]
rs2250557	0.83[EUR][1000 genomes]
rs2250666	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2529458	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2529459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2529465	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2529474	0.93[EUR][1000 genomes]
rs2681724	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681729	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2681732	0.86[EUR][1000 genomes]
rs2681738	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2681739	0.94[EUR][1000 genomes]
rs2681750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681756	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681758	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2681760	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2681763	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2681770	0.93[EUR][1000 genomes]
rs4899430	0.86[TSI][hapmap]
rs7151952	0.80[TSI][hapmap]
rs765221	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs769148	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs847325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs847328	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs847329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs847330	0.92[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs847331	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2139596	COQ6	cis	parietal	SCAN
rs2139596	DCAF4	cis	parietal	SCAN
rs2139596	NEK9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72818400-72824200	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr14:72818600-72824000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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