Variant report

Variant	rs1654559
Chromosome Location	chr19:51495686-51495687
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	chr19:51465646..51468437-chr19:51495218..51498068,3	MCF-7	breast:
2	chr19:51487899..51489635-chr19:51493828..51496214,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167755	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1532901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1612902	0.96[ASN][1000 genomes]
rs1627239	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1654519	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1654520	0.84[GIH][hapmap]
rs1654539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1654542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1654543	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1654558	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1698	0.83[MEX][hapmap]
rs1701914	0.96[ASN][1000 genomes]
rs1701916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1701919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1701920	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1701921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1701947	0.81[GIH][hapmap]
rs1701948	0.92[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.90[EUR][1000 genomes]
rs1722538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1722545	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1722546	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1722559	0.96[ASN][1000 genomes]
rs1722560	0.82[GIH][hapmap]
rs1722561	0.96[ASN][1000 genomes]
rs1722562	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1722563	0.96[ASN][1000 genomes]
rs1897605	0.96[ASN][1000 genomes]
rs1897606	0.96[ASN][1000 genomes]
rs2075802	0.87[JPT][hapmap]
rs2222554	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs2569441	0.88[CEU][hapmap]
rs2569456	0.84[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs2659071	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2659074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659095	0.84[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs2659096	0.84[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs268895	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs268899	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]
rs6509509	0.83[GIH][hapmap]
rs906190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1654559	NCR1	cis	parietal	SCAN
rs1654559	ZNF132	cis	parietal	SCAN
rs1654559	ZNF835	cis	parietal	SCAN
rs1654559	RPS5	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51493800-51496800	Enhancers	HMEC	breast
2	chr19:51494200-51498000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:51495000-51496600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr19:51495000-51496600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:51495200-51496400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:51495600-51496200	Flanking Active TSS	NHEK	skin

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