Variant report

Variant	rs12594941
Chromosome Location	chr15:56579268-56579269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56534615..56536116-chr15:56577645..56579684,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181827	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1031077	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs10518839	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs10518843	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1087838	0.85[GIH][hapmap];1.00[TSI][hapmap]
rs11071253	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs11629674	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs11631518	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs11632087	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs11632091	0.94[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11634404	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs11636040	0.84[CHB][hapmap];1.00[YRI][hapmap]
rs11637789	0.95[CHB][hapmap];0.87[YRI][hapmap]
rs12437864	0.95[CHB][hapmap];0.87[YRI][hapmap]
rs12439682	0.95[CHB][hapmap]
rs12439907	0.86[CHB][hapmap];0.87[YRI][hapmap]
rs12442539	0.95[CHB][hapmap]
rs12443042	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs12443429	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs12591303	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.85[YRI][hapmap]
rs12592096	0.95[CHB][hapmap]
rs12593348	1.00[EUR][1000 genomes]
rs12593453	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12593569	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs12595072	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs12595557	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs12595840	0.95[CHB][hapmap];0.87[YRI][hapmap]
rs1402173	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1550586	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs16976734	0.85[YRI][hapmap]
rs16976760	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs16976788	0.95[CHB][hapmap];0.87[YRI][hapmap]
rs16976847	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16976919	0.84[CHB][hapmap];0.88[CHD][hapmap];0.85[YRI][hapmap]
rs1863427	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867089	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1879344	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1879347	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1879348	0.95[CHB][hapmap]
rs1879349	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs2162216	1.00[CHB][hapmap]
rs2263567	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2554286	0.88[EUR][1000 genomes]
rs2682045	0.81[CHB][hapmap]
rs2713903	0.88[EUR][1000 genomes]
rs2718906	0.82[ASN][1000 genomes]
rs34431355	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3759868	0.85[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap]
rs4142479	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs4363812	0.86[CHB][hapmap];0.87[YRI][hapmap]
rs58851049	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59232912	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60861096	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7177904	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap]
rs748970	0.86[CHB][hapmap]
rs764014	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs8023554	1.00[CHB][hapmap];0.82[JPT][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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12594941	TUBB6	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56578800-56581600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:56579000-56582200	Weak transcription	Placenta	Placenta

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