Variant report

Variant	rs268899
Chromosome Location	chr19:51492089-51492090
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1532901	0.95[CEU][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1627239	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1654519	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654520	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1654521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1654543	0.82[GIH][hapmap]
rs1654559	0.88[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1701916	0.95[CEU][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1701919	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1701920	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1701921	0.96[CEU][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1701946	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1701947	0.84[GIH][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1701948	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1722538	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1722545	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1722546	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1722560	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1722562	0.82[EUR][1000 genomes]
rs2222554	0.80[CEU][hapmap]
rs2569439	0.85[CHB][hapmap]
rs2569441	0.92[CEU][hapmap]
rs2569443	0.84[CEU][hapmap]
rs2569456	0.80[CEU][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap]
rs2659071	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659074	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2659095	0.80[CEU][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap]
rs2659096	0.80[CEU][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap]
rs268893	0.99[ASN][1000 genomes]
rs268894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs268895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs268896	0.99[ASN][1000 genomes]
rs268897	0.99[ASN][1000 genomes]
rs268898	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2739429	0.84[CEU][hapmap]
rs6509509	0.81[GIH][hapmap]
rs906190	0.88[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs906191	0.92[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	nsv1064207	chr19:51474525-51497278	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1058277	chr19:51488544-51509847	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs268899	RPS5	cis	parietal	SCAN
rs268899	NCR1	cis	parietal	SCAN
rs268899	ZNF835	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51487400-51494200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:51487600-51492800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:51487600-51493800	Weak transcription	HMEC	breast

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