Variant report

Variant	rs2577067
Chromosome Location	chr18:28728384-28728385
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	chr18:28726707..28729377-chr18:28734464..28736505,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1370450	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1437605	0.84[EUR][1000 genomes]
rs1437608	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[EUR][1000 genomes]
rs1437609	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1437610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1437611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1437612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1816632	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1816633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2118341	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2118342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2118343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2164765	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2164766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254170	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2254172	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2577073	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2741004	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851996	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851999	0.82[ASW][hapmap]
rs4325646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4344831	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4361001	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6506886	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506891	0.89[JPT][hapmap]
rs6506892	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7238415	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243239	0.92[EUR][1000 genomes]
rs8090853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8096368	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951298	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs976749	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs976750	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs976751	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs991482	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9947328	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9948366	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9952351	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9955032	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9955430	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9959845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9960487	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530788	chr18:28596461-28751891	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv3360998	chr18:28693111-28881812	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3405228	chr18:28728154-28732452	ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2577067	DSC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28710600-28740800	Weak transcription	Primary T cells from cord blood	blood
2	chr18:28726600-28730000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr18:28726600-28734000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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