Variant report

Variant	rs1827011
Chromosome Location	chr11:9138129-9138130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9111940..9114012-chr11:9136709..9138771,2	MCF-7	breast:
2	chr11:9131566..9134213-chr11:9137062..9139541,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175356	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10047438	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1039210	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10769990	0.85[AFR][1000 genomes]
rs10769991	0.81[CHD][hapmap]
rs10769992	0.88[CEU][hapmap]
rs10769993	0.89[JPT][hapmap]
rs10769994	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10769997	0.81[EUR][1000 genomes]
rs10840174	1.00[ASN][1000 genomes]
rs10840175	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10840176	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10840183	0.81[EUR][1000 genomes]
rs11042189	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042200	0.83[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs12290916	0.84[ASN][1000 genomes]
rs12291375	0.81[EUR][1000 genomes]
rs1874822	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2133217	0.80[CEU][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2316087	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2647533	0.88[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2647535	0.84[EUR][1000 genomes]
rs2647537	0.92[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs2742556	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2742557	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3898554	0.85[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4910035	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5011703	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7109745	0.86[AMR][1000 genomes]
rs7128469	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7394878	0.87[MEX][hapmap]
rs7395151	0.84[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7395347	0.81[CHD][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7395846	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7396705	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7930507	0.80[CEU][hapmap];0.91[MEX][hapmap]
rs7931872	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7947251	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7948219	0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1827011	EIF4G2	cis	cerebellum	SCAN
rs1827011	TRIM5	cis	cerebellum	SCAN
rs1827011	OR56A1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9113600-9159800	Weak transcription	Right Ventricle	heart
2	chr11:9115000-9141800	Weak transcription	HSMM	muscle
3	chr11:9121800-9154800	Weak transcription	Brain Substantia Nigra	brain
4	chr11:9125000-9142800	Weak transcription	Left Ventricle	heart
5	chr11:9130800-9153600	Weak transcription	Brain Angular Gyrus	brain
6	chr11:9131200-9143000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:9132000-9153200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:9134000-9153000	Weak transcription	Brain Germinal Matrix	brain
9	chr11:9134000-9154000	Weak transcription	Osteobl	bone
10	chr11:9134200-9154000	Weak transcription	NHDF-Ad	bronchial
11	chr11:9134800-9142400	Weak transcription	Aorta	Aorta
12	chr11:9134800-9159000	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:9134800-9161200	Weak transcription	Fetal Brain Male	brain
14	chr11:9135000-9142000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:9135200-9152600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:9135400-9143000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr11:9135600-9142400	Weak transcription	Fetal Stomach	stomach
18	chr11:9135600-9153000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:9136200-9141200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:9136400-9159200	Weak transcription	Brain Anterior Caudate	brain
21	chr11:9136800-9143000	Weak transcription	Fetal Brain Female	brain
22	chr11:9137000-9142400	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:9137200-9145400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:9137200-9159000	Weak transcription	Fetal Heart	heart
25	chr11:9137800-9146200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:9138000-9142200	Weak transcription	K562	blood

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