Variant report

Variant	rs1399960
Chromosome Location	chr2:172484733-172484734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10185715	0.81[ASN][1000 genomes]
rs10432421	0.82[ASN][1000 genomes]
rs10432422	0.82[ASN][1000 genomes]
rs10432470	0.83[ASN][1000 genomes]
rs10432471	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10432472	0.82[ASN][1000 genomes]
rs10432473	0.80[ASN][1000 genomes]
rs11674857	0.82[ASN][1000 genomes]
rs11680728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11693157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12618717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622021	0.83[ASN][1000 genomes]
rs12991896	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12997634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13002792	0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13016328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13024519	0.84[JPT][hapmap]
rs13025856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473995	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs1533417	0.82[ASN][1000 genomes]
rs1554157	0.83[ASN][1000 genomes]
rs1554158	0.83[ASN][1000 genomes]
rs1969271	0.83[ASN][1000 genomes]
rs2037158	0.84[ASN][1000 genomes]
rs2037159	0.84[ASN][1000 genomes]
rs2037161	0.84[ASN][1000 genomes]
rs2037163	0.83[ASN][1000 genomes]
rs2102740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2138350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176150	0.82[ASN][1000 genomes]
rs2356796	0.81[ASN][1000 genomes]
rs2356797	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2884028	0.91[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28893802	0.82[ASN][1000 genomes]
rs34054455	0.90[ASN][1000 genomes]
rs34919335	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35735503	0.91[ASN][1000 genomes]
rs4264541	0.81[ASN][1000 genomes]
rs4265979	0.81[ASN][1000 genomes]
rs4265980	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4668395	0.82[ASN][1000 genomes]
rs4668396	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57130402	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59567105	0.81[ASN][1000 genomes]
rs62181734	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433301	0.81[ASN][1000 genomes]
rs6433302	0.81[ASN][1000 genomes]
rs6433305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704691	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6718546	0.82[ASN][1000 genomes]
rs6723896	0.81[ASN][1000 genomes]
rs6725338	0.82[ASN][1000 genomes]
rs6743208	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6747069	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6754595	0.83[ASN][1000 genomes]
rs7562302	0.83[ASN][1000 genomes]
rs7571192	0.82[ASN][1000 genomes]
rs7592639	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7606149	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7606189	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7606481	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs908371	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9287946	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9678221	0.83[ASN][1000 genomes]
rs997635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv997638	chr2:172442205-172560406	Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1399960	CHN1	cis	parietal	SCAN
rs1399960	ZAK	cis	parietal	SCAN
rs1399960	B3GALT1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172484200-172486000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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