Variant report

Variant	rs1654543
Chromosome Location	chr19:51498989-51498990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:51496140..51499135-chr19:51503262..51506454,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129455	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10420303	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs1532901	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1612902	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627239	1.00[ASN][1000 genomes]
rs1654520	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1654521	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1654539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654542	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654558	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1654559	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1701914	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1701915	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1701916	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1701919	0.99[ASN][1000 genomes]
rs1701920	0.99[ASN][1000 genomes]
rs1701921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1701946	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1701947	0.96[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs1701948	0.82[GIH][hapmap]
rs1722538	0.99[ASN][1000 genomes]
rs1722547	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1722559	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1722560	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]
rs1722561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1722562	0.99[ASN][1000 genomes]
rs1722563	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897605	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897606	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075802	0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap]
rs2222554	0.80[JPT][hapmap]
rs2569478	0.89[CEU][hapmap]
rs2659074	0.93[ASN][1000 genomes]
rs2659096	0.82[JPT][hapmap]
rs268893	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs268894	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs268896	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs268897	0.92[EUR][1000 genomes]
rs268898	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs268899	0.82[GIH][hapmap]
rs6509509	0.85[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap]
rs906190	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs906191	0.92[EUR][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
rs1654543	LILRB2	cis	cerebellum	SCAN
rs1654543	ZNF132	cis	parietal	SCAN
rs1654543	NCR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51496400-51499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:51496600-51499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr19:51496600-51502000	Weak transcription	NHEK	skin
4	chr19:51496600-51503000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:51498000-51502200	Weak transcription	HMEC	breast
6	chr19:51498000-51503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:51498600-51499400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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