Variant report

Variant	rs312952
Chromosome Location	chr2:21337857-21337858
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	chr2:21273537..21275484-chr2:21337666..21339362,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs312942	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs312946	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs312947	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs312948	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs312949	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs312950	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs312951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs312954	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs312955	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs312956	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs312957	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs312959	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs312962	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs312963	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs312971	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs312972	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs312973	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs312975	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs312977	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs312978	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs534100	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs563476	0.83[AFR][1000 genomes]
rs575905	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs581998	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645456	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs675430	0.83[AFR][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	nsv873728	chr2:21250914-21460786	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs312952	MSGN1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:21331800-21340600	Weak transcription	Liver	Liver
2	chr2:21337800-21338000	Enhancers	Gastric	stomach

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