Variant report

Variant	rs1722560
Chromosome Location	chr19:51500334-51500335
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10420303	0.92[CEU][hapmap];0.84[MEX][hapmap]
rs1532901	0.85[CEU][hapmap]
rs1612902	0.93[EUR][1000 genomes]
rs1654519	0.89[ASN][1000 genomes]
rs1654520	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1654521	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1654539	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1654542	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1654543	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1654559	0.82[GIH][hapmap]
rs1701914	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1701915	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1701946	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1701947	0.81[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1701948	0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs1722545	0.89[ASN][1000 genomes]
rs1722546	0.90[ASN][1000 genomes]
rs1722547	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1722559	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1722561	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1722563	0.93[EUR][1000 genomes]
rs1897605	0.93[EUR][1000 genomes]
rs1897606	0.93[EUR][1000 genomes]
rs2075802	0.96[CEU][hapmap]
rs2569478	0.88[CEU][hapmap]
rs2659071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs268893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs268894	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs268895	0.90[ASN][1000 genomes]
rs268896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs268897	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs268898	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs268899	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6509509	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs906190	0.82[GIH][hapmap]
rs906191	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs952108	0.92[CEU][hapmap]
rs952109	0.92[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs1722560	NCR1	cis	parietal	SCAN
rs1722560	ZNF132	cis	parietal	SCAN
rs1722560	LILRB2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51496600-51502000	Weak transcription	NHEK	skin
2	chr19:51496600-51503000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:51498000-51502200	Weak transcription	HMEC	breast
4	chr19:51498000-51503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:51499200-51500400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:51499200-51501600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:51499800-51503200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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