Variant report

Variant	rs1609519
Chromosome Location	chr1:97781039-97781040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10783059	0.90[EUR][1000 genomes]
rs10783060	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11808765	0.85[EUR][1000 genomes]
rs28696953	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs471581	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs499009	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs507170	0.92[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs526645	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs553388	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55651621	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61786317	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61786318	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61786353	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61786356	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61786357	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61787962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61787963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61787976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61787980	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61787981	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs628959	0.92[CEU][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs644023	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6660936	0.81[AMR][1000 genomes]
rs693680	0.82[ASW][hapmap];0.84[CEU][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs72726678	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72726691	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7518848	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7524482	0.85[EUR][1000 genomes]
rs7526933	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7556439	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs827500	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv869751	chr1:97749598-97790476	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1609519	DBT	cis	parietal	SCAN
rs1609519	LPPR4	cis	parietal	SCAN
rs1609519	GPR88	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97769200-97781800	Weak transcription	NHLF	lung
2	chr1:97770400-97797600	Weak transcription	HSMM	muscle
3	chr1:97771000-97782400	Weak transcription	Primary B cells from cord blood	blood
4	chr1:97771400-97781400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:97772000-97781200	Weak transcription	Dnd41	blood
6	chr1:97774000-97783200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:97780200-97781600	Strong transcription	Primary T cells from cord blood	blood
8	chr1:97780400-97781800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:97780600-97807200	Weak transcription	Primary monocytes fromperipheralblood	blood

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