Variant report

Variant	rs6438087
Chromosome Location	chr3:112366816-112366817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112357844..112361438-chr3:112364098..112368101,7	MCF-7	breast:
2	chr3:112364416..112367219-chr3:112696303..112699489,3	MCF-7	breast:
3	chr3:112364472..112367119-chr3:112708637..112711518,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272844	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2279531	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6438086	0.91[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6772337	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs6794305	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6807798	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7611898	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7620601	0.87[TSI][hapmap]
rs9683135	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9815819	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9821100	0.85[CHD][hapmap]
rs9821338	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs9870933	0.89[TSI][hapmap]

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
rs6438087	BOC	cis	cerebellum	SCAN
rs6438087	ESAM	trans	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112360800-112367800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:112362400-112367600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:112362400-112367800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:112362800-112367800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:112363400-112373600	Weak transcription	Esophagus	oesophagus
6	chr3:112363800-112368000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:112364600-112372800	Enhancers	Osteobl	bone
8	chr3:112365000-112367000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:112365000-112367200	Enhancers	Adipose Nuclei	Adipose
10	chr3:112365000-112367200	Enhancers	NH-A	brain
11	chr3:112365000-112370600	Enhancers	NHLF	lung
12	chr3:112365200-112367000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:112365200-112367000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:112365200-112367000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:112365200-112367000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:112365200-112367000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:112365200-112367000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:112365200-112367400	Enhancers	HMEC	breast
19	chr3:112365200-112368200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:112365200-112368400	Enhancers	Placenta	Placenta
21	chr3:112365200-112369600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:112365200-112370600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:112365400-112367000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:112365400-112367000	Enhancers	H9 Cell Line	embryonic stem cell
25	chr3:112365400-112367000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:112365400-112367000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr3:112365400-112367000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:112365400-112367000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:112365400-112367000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:112365400-112367200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:112365400-112368200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:112365600-112367000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:112365600-112367000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:112365600-112367000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr3:112365800-112367000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:112366000-112367000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr3:112366000-112367800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:112366200-112367000	Flanking Active TSS	HSMM	muscle
39	chr3:112366200-112367000	Flanking Active TSS	HSMMtube	muscle
40	chr3:112366400-112367000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr3:112366400-112367000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr3:112366400-112367000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr3:112366400-112367000	Enhancers	Fetal Heart	heart
44	chr3:112366400-112367000	Enhancers	NHEK	skin
45	chr3:112366400-112367800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:112366400-112372000	Weak transcription	Fetal Lung	lung
47	chr3:112366400-112372400	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:112366400-112372600	Enhancers	NHDF-Ad	bronchial
49	chr3:112366400-112373800	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:112366600-112367800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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