Variant report

Variant	rs1873554
Chromosome Location	chr6:120218447-120218448
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	chr6:120202928..120204713-chr6:120216019..120218723,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12194033	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1330108	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1330109	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1330112	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1330114	0.81[ASN][1000 genomes]
rs2149974	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2357756	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357757	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2357758	0.86[ASN][1000 genomes]
rs2357759	0.87[ASN][1000 genomes]
rs2884263	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2884264	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5021039	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5021040	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5021041	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5021042	0.87[ASN][1000 genomes]
rs6569092	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902508	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6904279	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904839	0.87[ASN][1000 genomes]
rs6915356	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6915714	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6924955	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6928479	0.89[ASN][1000 genomes]
rs6932256	0.87[ASN][1000 genomes]
rs7738340	0.81[ASN][1000 genomes]
rs7750148	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756951	0.81[ASN][1000 genomes]
rs7768469	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7772450	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7772500	0.81[ASN][1000 genomes]
rs7774016	0.87[ASN][1000 genomes]
rs7776192	0.86[ASN][1000 genomes]
rs9320717	0.85[ASN][1000 genomes]
rs9320718	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9320719	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs937091	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9372567	0.87[ASN][1000 genomes]
rs9372568	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9374841	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9374843	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9374844	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9385100	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9387689	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9387690	0.87[ASN][1000 genomes]
rs9387691	0.87[ASN][1000 genomes]
rs9398532	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9398533	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9398534	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9401183	0.81[ASN][1000 genomes]
rs9401185	0.81[ASN][1000 genomes]
rs9401186	0.87[ASN][1000 genomes]
rs9401187	0.87[ASN][1000 genomes]
rs9401189	0.90[ASN][1000 genomes]
rs9489826	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9489827	0.87[ASN][1000 genomes]
rs952212	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs952213	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[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	nsv886572	chr6:120165475-120284480	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv2763951	chr6:120195400-120297444	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2830171	chr6:120200969-120233977	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1873554	COL10A1	cis	parietal	SCAN
rs1873554	SLC35F1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:120216200-120230600	Weak transcription	Fetal Lung	lung
2	chr6:120216800-120219600	Weak transcription	Placenta	Placenta
3	chr6:120218400-120218800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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