Variant report

Variant	rs3825082
Chromosome Location	chr12:11914747-11914748
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11905328..11907966-chr12:11912733..11915677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11054443	0.80[CEU][hapmap]
rs11615083	0.84[CEU][hapmap]
rs1547393	0.81[CEU][hapmap]
rs17210559	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2051524	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs3782137	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4763723	0.84[ASW][hapmap];0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7310017	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs974728	0.83[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv1053609	chr12:11898099-11933906	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv469113	chr12:11913360-11931259	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv557574	chr12:11913360-11931259	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3825082	PLBD1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11893200-11915000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:11900600-11915000	Weak transcription	NHEK	skin
3	chr12:11904000-11918000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:11905800-11918400	Weak transcription	Fetal Brain Male	brain
5	chr12:11906400-11918600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:11906800-11915000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:11906800-11915000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:11907000-11917200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:11907600-11918200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:11907800-11915000	Weak transcription	HMEC	breast
11	chr12:11908000-11918800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:11908200-11918800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:11908600-11915000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:11908600-11931800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:11909200-11915000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:11909200-11915800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:11909200-11919400	Weak transcription	Liver	Liver
18	chr12:11909400-11914800	Weak transcription	HSMM	muscle
19	chr12:11909400-11915200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:11909400-11915400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:11909400-11915600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:11909400-11915800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:11909400-11916600	Weak transcription	NHDF-Ad	bronchial
24	chr12:11909600-11915000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:11909600-11915200	Weak transcription	Osteobl	bone
26	chr12:11909600-11932400	Genic enhancers	Fetal Thymus	thymus
27	chr12:11909800-11914800	Weak transcription	A549	lung
28	chr12:11909800-11919000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:11910600-11916800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr12:11911000-11915000	Weak transcription	Colonic Mucosa	Colon
31	chr12:11911000-11915200	Weak transcription	Esophagus	oesophagus
32	chr12:11911600-11915000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:11911800-11915000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:11911800-11915000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:11911800-11915200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:11912000-11914800	Weak transcription	Primary T cells from cord blood	blood
37	chr12:11912000-11915000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr12:11912000-11915000	Weak transcription	Placenta	Placenta
39	chr12:11912000-11915000	Weak transcription	Pancreas	Pancrea
40	chr12:11912000-11916000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:11912000-11916600	Weak transcription	Fetal Kidney	kidney
42	chr12:11912000-11917600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:11912000-11918600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:11912400-11915000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:11912400-11915000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr12:11912400-11915000	Weak transcription	Lung	lung
47	chr12:11912400-11915000	Weak transcription	HUVEC	blood vessel
48	chr12:11912400-11915400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:11912400-11916400	Weak transcription	Fetal Lung	lung
50	chr12:11912400-11918800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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