Variant report

Variant	rs12712304
Chromosome Location	chr2:31267391-31267392
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31265375..31268101-chr2:31269640..31272936,3	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10194342	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10197865	0.80[MEX][hapmap]
rs10198054	0.91[CEU][hapmap]
rs10205584	0.95[ASN][1000 genomes]
rs10205676	0.94[ASN][1000 genomes]
rs10209881	0.83[MEX][hapmap]
rs11124237	0.94[ASN][1000 genomes]
rs11688387	0.87[ASN][1000 genomes]
rs11694302	0.95[ASN][1000 genomes]
rs11886970	0.95[ASN][1000 genomes]
rs11891469	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11898944	0.95[ASN][1000 genomes]
rs12464083	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12613732	0.91[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12617279	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619377	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12621518	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12621546	0.91[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12621813	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12712300	0.92[MEX][hapmap]
rs12712301	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12712302	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12712303	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12712305	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712306	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12992642	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13009298	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1862966	0.83[MEX][hapmap]
rs1862967	0.87[MEX][hapmap]
rs1862983	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2194455	0.91[CEU][hapmap]
rs4245766	0.84[MEX][hapmap]
rs4268964	0.97[ASN][1000 genomes]
rs4951960	0.87[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs4951961	0.95[ASN][1000 genomes]
rs4952040	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4952043	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4952045	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs58091345	0.93[ASN][1000 genomes]
rs61456515	0.89[ASN][1000 genomes]
rs62140633	0.95[ASN][1000 genomes]
rs6705225	0.84[ASN][1000 genomes]
rs6726690	0.95[ASN][1000 genomes]
rs6730186	0.95[ASN][1000 genomes]
rs6734015	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72793304	0.95[ASN][1000 genomes]
rs7605643	0.83[MEX][hapmap]
rs7605982	0.83[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs9679162	0.80[MEX][hapmap]

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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12712304	GALNT14	cis	parietal	SCAN
rs12712304	FAM179A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31251400-31270000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:31262000-31272200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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