Variant report

Variant	rs1554158
Chromosome Location	chr2:172477711-172477712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10185715	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10432421	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10432422	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10432469	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10432470	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10432471	0.87[ASN][1000 genomes]
rs10432472	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10432473	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930486	0.93[ASN][1000 genomes]
rs11674857	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11680728	0.83[ASN][1000 genomes]
rs11683762	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs11693157	0.84[ASN][1000 genomes]
rs12618717	0.84[ASN][1000 genomes]
rs12622021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12991896	0.83[ASN][1000 genomes]
rs12996145	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs12997634	0.84[ASN][1000 genomes]
rs13002792	0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs13016328	0.84[ASN][1000 genomes]
rs13024519	0.94[JPT][hapmap]
rs13025856	0.84[ASN][1000 genomes]
rs1399960	0.83[ASN][1000 genomes]
rs1473995	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs1533417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543128	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1554157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1606926	0.93[ASN][1000 genomes]
rs1969271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037158	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037159	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037160	0.95[ASN][1000 genomes]
rs2037161	0.98[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2037163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2102739	0.92[ASN][1000 genomes]
rs2102740	0.84[ASN][1000 genomes]
rs2138350	0.83[ASN][1000 genomes]
rs2176150	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2356796	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884028	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs28893802	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34054455	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35735503	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4264541	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4265979	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4265980	0.81[ASN][1000 genomes]
rs4668395	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668396	0.83[ASN][1000 genomes]
rs4668397	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59567105	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6433301	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433302	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433305	0.83[ASN][1000 genomes]
rs6704691	0.86[ASN][1000 genomes]
rs6718546	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6723896	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6725338	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743208	0.83[ASN][1000 genomes]
rs6745725	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs6747069	0.84[ASN][1000 genomes]
rs6754595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562302	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571192	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7575168	0.93[ASN][1000 genomes]
rs7592639	0.83[ASN][1000 genomes]
rs7606149	0.83[ASN][1000 genomes]
rs7606189	0.81[ASN][1000 genomes]
rs7606481	0.83[ASN][1000 genomes]
rs908371	0.82[ASN][1000 genomes]
rs9287946	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9678221	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs997635	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv821788	chr2:172476049-172478198	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1554158	B3GALT1	cis	parietal	SCAN
rs1554158	CD226	trans	cerebellum	SCAN
rs1554158	METTL8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172469000-172482600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:172477400-172477800	Enhancers	HSMMtube	muscle

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