Variant report

Variant	rs3898554
Chromosome Location	chr11:9133052-9133053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9130567..9133268-chr11:9383092..9385997,2	MCF-7	breast:
2	chr11:9131737..9134967-chr11:9139541..9142848,3	MCF-7	breast:
3	chr11:9131566..9134213-chr11:9137062..9139541,3	MCF-7	breast:
4	chr11:9129578..9133979-chr11:9156712..9160825,5	MCF-7	breast:
5	chr11:9123650..9128342-chr11:9129047..9134546,16	MCF-7	breast:
6	chr11:9126109..9129773-chr11:9130849..9133225,4	K562	blood:
7	chr11:9131112..9133344-chr11:9145799..9148369,2	MCF-7	breast:
8	chr11:9126109..9129789-chr11:9130849..9133587,3	K562	blood:

Variant related genes	Relation type
ENSG00000175356	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10769991	0.91[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10769993	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10769995	0.81[EUR][1000 genomes]
rs10769996	0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10840174	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10840175	0.82[ASN][1000 genomes]
rs10840178	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10840179	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11042189	0.88[ASN][1000 genomes]
rs11042195	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11042200	0.89[JPT][hapmap]
rs11604616	0.91[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12286943	0.88[JPT][hapmap]
rs1353730	0.92[GIH][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs17256375	0.86[MEX][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1827011	0.85[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1997628	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2316087	0.88[ASN][1000 genomes]
rs2316088	0.88[JPT][hapmap]
rs2742467	0.82[EUR][1000 genomes]
rs5011703	0.90[ASN][1000 genomes]
rs7123970	0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs7395151	1.00[JPT][hapmap]
rs7395347	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7930192	0.88[JPT][hapmap]
rs7931872	0.80[ASN][1000 genomes]
rs7948219	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3898554	OR56A1	cis	cerebellum	SCAN
rs3898554	OR10A6	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9113600-9159800	Weak transcription	Right Ventricle	heart
2	chr11:9114200-9136200	Weak transcription	Fetal Heart	heart
3	chr11:9115000-9141800	Weak transcription	HSMM	muscle
4	chr11:9115200-9134400	Weak transcription	Fetal Stomach	stomach
5	chr11:9121800-9154800	Weak transcription	Brain Substantia Nigra	brain
6	chr11:9125000-9142800	Weak transcription	Left Ventricle	heart
7	chr11:9128000-9134600	Weak transcription	Aorta	Aorta
8	chr11:9130800-9153600	Weak transcription	Brain Angular Gyrus	brain
9	chr11:9131200-9133400	Weak transcription	Brain Germinal Matrix	brain
10	chr11:9131200-9143000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:9132000-9153200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:9132800-9133200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:9132800-9133600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:9133000-9133400	ZNF genes & repeats	Psoas Muscle	Psoas
15	chr11:9133000-9133800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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