Variant report

Variant	rs1383819
Chromosome Location	chr8:51371466-51371467
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10957935	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10957941	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1114808	0.82[MEX][hapmap]
rs11785117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs12541396	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12547235	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12547263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13276494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs13280891	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542614	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16919578	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1843005	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1843006	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1843007	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1904996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1904997	0.82[MEX][hapmap]
rs1994032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2086517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs218876	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2392700	1.00[CEU][hapmap]
rs2448934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2448935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2448937	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2448940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2448941	0.82[MEX][hapmap]
rs2467203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2623209	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2623212	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2623213	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2623214	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2623220	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2623221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2623222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2625733	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2625740	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2625754	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2625756	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2625757	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2625758	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs310562	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs310575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs310576	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs310577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34880125	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4873148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7827319	0.82[MEX][hapmap]
rs996521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs996522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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
3	nsv831312	chr8:51239772-51422844	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916262	chr8:51322341-51437077	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv520800	chr8:51365953-51371910	Weak transcription Bivalent Enhancer Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1383819	SNAI2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:51365800-51375800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:51370600-51374400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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