Variant report

Variant	rs3133855
Chromosome Location	chr11:120584851-120584852
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	chr11:120584157..120585682-chr11:120588505..120590152,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10892618	0.95[MEX][hapmap]
rs10892619	0.83[EUR][1000 genomes]
rs10892620	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11217977	0.82[EUR][1000 genomes]
rs17245664	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs2852225	0.86[YRI][hapmap]
rs2852227	0.86[YRI][hapmap]
rs3133856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054407	chr11:120535570-120630114	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3693392	chr11:120549745-120628012	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1041465	chr11:120582595-120630114	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv541180	chr11:120582595-120630114	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv1038264	chr11:120582595-120799335	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv541181	chr11:120582595-120799335	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3133855	ARHGEF12	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120579200-120585200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr11:120580000-120585800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:120581000-120585200	Enhancers	Fetal Kidney	kidney
4	chr11:120581000-120585800	Enhancers	Ovary	ovary
5	chr11:120581800-120585800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:120582000-120585000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:120582200-120585600	Weak transcription	Brain Angular Gyrus	brain
8	chr11:120582200-120585600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:120582200-120585800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:120582200-120587200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:120582200-120587200	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:120582200-120588800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:120582400-120585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:120582800-120585800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:120583000-120585800	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:120583000-120585800	Weak transcription	Colonic Mucosa	Colon
17	chr11:120583200-120585600	Weak transcription	Adipose Nuclei	Adipose
18	chr11:120583600-120585800	Weak transcription	NHLF	lung
19	chr11:120583800-120585000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:120583800-120585000	Weak transcription	GM12878-XiMat	blood
21	chr11:120583800-120585200	Weak transcription	HepG2	liver
22	chr11:120583800-120585600	Weak transcription	NHDF-Ad	bronchial
23	chr11:120583800-120585800	Enhancers	Fetal Intestine Small	intestine
24	chr11:120584000-120585800	Enhancers	Fetal Intestine Large	intestine
25	chr11:120584200-120586800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr11:120584600-120585600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:120584800-120585000	Enhancers	H9 Cell Line	embryonic stem cell
28	chr11:120584800-120585000	Enhancers	Brain Substantia Nigra	brain

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