Variant report

Variant	rs2681754
Chromosome Location	chr14:72819684-72819685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10138180	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1072167	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1099968	0.80[ASW][hapmap]
rs12892244	0.82[JPT][hapmap]
rs1356843	0.80[TSI][hapmap]
rs1520331	0.96[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs1520332	0.96[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2079504	0.80[TSI][hapmap]
rs2079505	0.80[TSI][hapmap]
rs2079506	0.80[TSI][hapmap]
rs2090737	0.92[CEU][hapmap]
rs2108361	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2108362	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2190508	0.80[ASW][hapmap]
rs2214965	0.84[ASW][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2238199	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2239224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239225	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239229	0.89[ASW][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2239230	0.80[EUR][1000 genomes]
rs2239231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2239233	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2239248	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2239249	0.92[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2283385	0.89[ASW][hapmap];0.80[MEX][hapmap]
rs2283390	0.96[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs2332829	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2332831	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2529460	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2529461	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2529466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2529467	1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2681728	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2681731	0.80[TSI][hapmap]
rs2681741	1.00[YRI][hapmap]
rs2681742	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2681743	1.00[YRI][hapmap]
rs2681748	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2681749	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2681751	1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2681752	1.00[YRI][hapmap]
rs2681753	0.80[EUR][1000 genomes]
rs2681761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2681765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681767	0.80[TSI][hapmap]
rs2681768	0.80[TSI][hapmap]
rs4903013	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6574067	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6574068	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6574070	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6574071	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7146606	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7149872	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8022289	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs847326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs847327	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs847332	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs847333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs847354	0.82[TSI][hapmap]
rs929413	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv2757573	chr14:72802736-72819684	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2759995	chr14:72802736-72819684	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2681754	PCNX	cis	parietal	SCAN
rs2681754	TMED10	cis	parietal	SCAN
rs2681754	C14orf115	cis	cerebellum	SCAN
rs2681754	C14orf43	cis	cerebellum	SCAN

Chromatin state (count:3 , 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
3	chr14:72819400-72822000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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