Variant report

Variant	rs12451513
Chromosome Location	chr17:59642328-59642329
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120728742..120730262-chr17:59641665..59643823,2	MCF-7	breast:
2	chr17:59641783..59644621-chr17:60141604..60143594,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10438755	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10438756	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11650703	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11654397	0.81[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11655330	0.85[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11869403	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12451827	0.95[MEX][hapmap];0.80[TSI][hapmap]
rs12452859	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12939687	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12941500	0.86[ASW][hapmap];0.85[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12949631	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12952180	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1476799	0.81[EUR][1000 genomes]
rs1476800	0.87[MEX][hapmap]
rs1558275	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1558276	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1860414	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2378870	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2378871	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4583315	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8064466	0.80[ASW][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8070532	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071653	0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs977745	0.87[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457864	chr17:59612041-59646764	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
2	nsv575840	chr17:59612041-59646764	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12451513	TRIM25	cis	parietal	SCAN
rs12451513	MRPS23	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59634000-59646200	Weak transcription	Stomach Mucosa	stomach
2	chr17:59639400-59642400	Weak transcription	A549	lung

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