Variant report

Variant	rs7517726
Chromosome Location	chr1:172913577-172913578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172908894..172911352-chr1:172913551..172915186,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10489274	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10798242	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10798243	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10912497	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10912499	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912501	0.83[EUR][1000 genomes]
rs10912502	0.80[EUR][1000 genomes]
rs12035082	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12037203	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12037606	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12088638	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12402215	0.83[EUR][1000 genomes]
rs12407389	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12409216	0.80[EUR][1000 genomes]
rs12410129	0.82[EUR][1000 genomes]
rs12565596	0.82[EUR][1000 genomes]
rs1894636	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2179425	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2206364	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2206365	0.83[EUR][1000 genomes]
rs2206366	0.82[EUR][1000 genomes]
rs2213746	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2422257	0.90[CHD][hapmap];0.87[GIH][hapmap]
rs2422260	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4145469	0.96[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4916199	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4916286	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4916289	0.83[EUR][1000 genomes]
rs4916290	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425189	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6674470	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6688532	0.96[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7539319	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7539951	0.82[EUR][1000 genomes]
rs926472	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs926473	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs926474	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9283384	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv831904	chr1:172912110-173070429	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7517726	C1orf114	cis	parietal	SCAN
rs7517726	SNORD47	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172903600-172914200	Weak transcription	Aorta	Aorta
2	chr1:172905600-172916000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:172910800-172914200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:172910800-172916200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:172911000-172914400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:172911200-172914200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:172911200-172914400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:172911200-172915800	Weak transcription	NHDF-Ad	bronchial
9	chr1:172911200-172916000	Weak transcription	HSMMtube	muscle
10	chr1:172911200-172916200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:172911200-172917000	Weak transcription	Fetal Stomach	stomach
12	chr1:172911200-172917600	Weak transcription	Fetal Lung	lung
13	chr1:172911400-172916000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:172911400-172916000	Weak transcription	NH-A	brain

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