Variant report

Variant	rs1483643
Chromosome Location	chr8:51459757-51459758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10808836	0.90[ASN][1000 genomes]
rs10957914	1.00[CHB][hapmap]
rs10957915	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs10957916	0.86[CHB][hapmap];0.83[TSI][hapmap]
rs1114500	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1114808	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap]
rs11775411	0.80[AMR][1000 genomes]
rs11781401	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap]
rs12545254	0.85[AMR][1000 genomes]
rs12546744	0.93[CHB][hapmap]
rs12546758	0.90[AMR][1000 genomes]
rs13248847	0.90[AMR][1000 genomes]
rs13251708	0.88[AMR][1000 genomes]
rs13258865	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs13274680	0.80[AMR][1000 genomes]
rs1383815	0.82[CHB][hapmap]
rs1471578	0.84[TSI][hapmap]
rs1481467	0.82[CHB][hapmap]
rs1481468	0.82[CHB][hapmap]
rs1481472	0.95[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs1481482	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483636	0.90[AMR][1000 genomes]
rs1483644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1483645	0.90[AMR][1000 genomes]
rs1542613	0.90[AMR][1000 genomes]
rs1542615	0.86[GIH][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes]
rs1904997	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap]
rs192844	0.87[AMR][1000 genomes]
rs1971259	0.86[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes]
rs1994031	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062038	0.86[CHB][hapmap]
rs2068238	0.90[AMR][1000 genomes]
rs2128000	1.00[CHB][hapmap]
rs2170373	0.82[CHB][hapmap]
rs2251415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392627	0.86[CHB][hapmap];0.80[TSI][hapmap]
rs2392699	0.94[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes]
rs2448936	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2448941	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap]
rs2467205	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2623207	0.86[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes]
rs2623208	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2623210	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623211	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2623215	0.90[AMR][1000 genomes]
rs2623216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2623224	0.83[GIH][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes]
rs2623225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625736	1.00[CHB][hapmap]
rs2625739	0.90[AMR][1000 genomes]
rs2625750	0.90[AMR][1000 genomes]
rs2625751	0.90[AMR][1000 genomes]
rs2625752	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2625753	0.90[AMR][1000 genomes]
rs2625755	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2930096	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310557	0.90[AMR][1000 genomes]
rs310558	1.00[CHB][hapmap]
rs310574	0.86[GIH][hapmap];0.84[TSI][hapmap]
rs4440649	0.95[MEX][hapmap]
rs4442158	1.00[CHB][hapmap]
rs4577970	0.89[MEX][hapmap];0.80[TSI][hapmap];0.90[AMR][1000 genomes]
rs4873147	0.84[TSI][hapmap]
rs4873149	0.80[AMR][1000 genomes]
rs4873457	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs4873458	0.84[TSI][hapmap]
rs4873459	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs6983589	0.86[CHB][hapmap]
rs6997739	0.82[CHB][hapmap]
rs7007612	0.85[AMR][1000 genomes]
rs7009024	0.86[CHB][hapmap]
rs7015139	0.92[CHB][hapmap]
rs7817955	0.84[MEX][hapmap];0.84[TSI][hapmap]
rs7827319	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]
rs7842092	0.86[CHB][hapmap]
rs9298323	0.86[CHB][hapmap]
rs9650165	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs9650166	0.86[CHB][hapmap]
rs996523	0.82[AMR][1000 genomes]
rs996524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948436	chr8:51115028-51917504	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv429914	chr8:51371447-51617647	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv531502	chr8:51390997-51703556	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3514165	chr8:51416583-51923545	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3514166	chr8:51416583-51923545	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1029576	chr8:51418003-51476385	ZNF genes & repeats Strong transcription Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1022304	chr8:51442784-51475071	ZNF genes & repeats Enhancers Weak transcription Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
8	nsv539608	chr8:51442784-51475071	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
9	nsv1030044	chr8:51442827-51476385	ZNF genes & repeats Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1483643	PXDNL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:51441000-51469200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:51457400-51469400	Weak transcription	Brain Germinal Matrix	brain
3	chr8:51458200-51469400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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