Variant report

Variant	rs12491378
Chromosome Location	chr3:156946257-156946258
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	chr3:156937140..156939016-chr3:156942989..156946437,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10936082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs11709487	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11718332	0.82[MEX][hapmap]
rs12489852	0.81[EUR][1000 genomes]
rs12490031	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1500913	0.82[MEX][hapmap]
rs1500914	0.82[MEX][hapmap]
rs1500926	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17388505	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2305621	0.82[ASW][hapmap];0.91[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs34650246	0.82[EUR][1000 genomes]
rs56003856	0.84[EUR][1000 genomes]
rs56375731	0.83[EUR][1000 genomes]
rs61473987	0.87[EUR][1000 genomes]
rs62279638	0.87[EUR][1000 genomes]
rs62279639	0.87[EUR][1000 genomes]
rs62279641	0.83[EUR][1000 genomes]
rs62281371	0.82[EUR][1000 genomes]
rs62281372	0.82[EUR][1000 genomes]
rs62281373	0.82[EUR][1000 genomes]
rs67643214	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6769039	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6793166	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6803886	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs73154644	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154694	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7618171	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9864194	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12491378	BRD7	cis	parietal	SCAN
rs12491378	KCNAB1	cis	cerebellum	SCAN
rs12491378	SSR3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156938200-156948400	Weak transcription	NHDF-Ad	bronchial
2	chr3:156944600-156948400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:156944600-156948400	Weak transcription	Osteobl	bone
4	chr3:156944600-156948600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:156944800-156948400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:156946200-156947200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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