Variant report

Variant	rs9821338
Chromosome Location	chr3:112375450-112375451
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	chr3:112362097..112368318-chr3:112369170..112375638,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11927615	0.90[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs12054001	0.91[EUR][1000 genomes]
rs12054416	0.95[CEU][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1249910	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs13068244	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13077054	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13088866	0.89[EUR][1000 genomes]
rs13092258	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2279531	0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs60397548	0.89[EUR][1000 genomes]
rs6438086	0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6438087	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs6794305	0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6807798	0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7611898	0.89[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs9683135	0.89[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs9815819	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs9818848	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9821100	0.89[CHD][hapmap]
rs9821161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833456	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9859566	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9864580	0.84[EUR][1000 genomes]
rs9864774	0.93[EUR][1000 genomes]
rs9876497	0.85[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes];0.87[EUR][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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9821338	ESAM	trans	parietal	SCAN
rs9821338	BOC	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112372400-112380600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:112373400-112376800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:112373800-112376400	Enhancers	NHDF-Ad	bronchial
4	chr3:112375000-112377400	Weak transcription	NHLF	lung
5	chr3:112375000-112389000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:112375200-112376600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:112375400-112376600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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