Variant report

Variant	rs11706377
Chromosome Location	chr3:138640704-138640705
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	chr3:138311406..138314076-chr3:138638843..138641215,2	MCF-7	breast:
2	chr3:138633432..138635539-chr3:138639300..138641799,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114107	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1021135	0.83[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10935293	0.85[ASN][1000 genomes]
rs11919606	0.85[ASN][1000 genomes]
rs11919625	0.85[ASN][1000 genomes]
rs11923711	0.85[ASN][1000 genomes]
rs12485482	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12487074	0.85[ASN][1000 genomes]
rs12695690	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1976037	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2062159	0.85[ASN][1000 genomes]
rs4453869	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4894365	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs4894366	0.83[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs4894367	0.83[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs4894368	0.85[ASN][1000 genomes]
rs4894369	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4894370	0.87[ASN][1000 genomes]
rs59509299	0.81[ASN][1000 genomes]
rs59746662	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439828	0.81[CEU][hapmap]
rs67386737	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779898	0.85[ASN][1000 genomes]
rs727191	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72975151	0.81[ASN][1000 genomes]
rs72975160	0.81[ASN][1000 genomes]
rs72975167	0.81[ASN][1000 genomes]
rs72975185	0.87[ASN][1000 genomes]
rs72975188	0.87[ASN][1000 genomes]
rs72975190	0.87[ASN][1000 genomes]
rs72975192	0.87[ASN][1000 genomes]
rs73231625	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7627822	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7628753	0.81[ASN][1000 genomes]
rs7631910	0.85[ASN][1000 genomes]
rs7632846	0.85[ASN][1000 genomes]
rs7637710	0.87[ASN][1000 genomes]
rs9809657	0.83[EUR][1000 genomes]
rs9820131	0.84[EUR][1000 genomes]
rs9840090	0.85[ASN][1000 genomes]
rs9877882	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11706377	ESYT3	cis	cerebellum	SCAN
rs11706377	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs11706377	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs11706377	FAIM	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138635200-138642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:138635200-138642600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:138635200-138642600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:138635200-138652600	Weak transcription	Ovary	ovary
5	chr3:138635200-138654800	Weak transcription	Right Atrium	heart
6	chr3:138636000-138642400	Weak transcription	K562	blood
7	chr3:138640000-138641600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:138640000-138641600	Enhancers	HMEC	breast
9	chr3:138640200-138641000	Enhancers	Placenta Amnion	Placenta Amnion
10	chr3:138640200-138641000	Enhancers	HUVEC	blood vessel
11	chr3:138640200-138641200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:138640200-138641200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:138640200-138641200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:138640200-138641200	Enhancers	A549	lung
15	chr3:138640200-138641200	Enhancers	HepG2	liver
16	chr3:138640200-138641200	Enhancers	HSMMtube	muscle
17	chr3:138640200-138641400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:138640200-138641400	Enhancers	NHEK	skin
19	chr3:138640200-138641600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:138640200-138641600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:138640200-138641600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:138640200-138641600	Enhancers	HSMM	muscle
23	chr3:138640200-138641600	Enhancers	NHDF-Ad	bronchial
24	chr3:138640200-138641600	Enhancers	NHLF	lung
25	chr3:138640200-138642600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:138640200-138642800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:138640400-138640800	Flanking Active TSS	NH-A	brain
28	chr3:138640400-138640800	Flanking Active TSS	Osteobl	bone
29	chr3:138640400-138641200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:138640400-138641200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:138640600-138640800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:138640600-138640800	Flanking Active TSS	Hela-S3	cervix
33	chr3:138640600-138641200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr3:138640600-138642400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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