Variant report

Variant	rs7964582
Chromosome Location	chr12:48359527-48359528
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	chr12:48296295..48301288-chr12:48356017..48360451,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10875712	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11609253	0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs4760607	1.00[CHB][hapmap]
rs4760674	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7964582	VDR	cis	parietal	SCAN
rs7964582	C12orf68	cis	parietal	SCAN
rs7964582	AQP6	cis	parietal	SCAN
rs7964582	DNAJC22	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358000-48359600	Flanking Active TSS	Fetal Intestine Small	intestine
2	chr12:48358200-48359600	Weak transcription	Gastric	stomach
3	chr12:48358200-48359600	Weak transcription	Left Ventricle	heart
4	chr12:48358200-48359600	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr12:48358200-48359800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:48358200-48359800	Enhancers	Right Atrium	heart
7	chr12:48358200-48359800	Enhancers	Spleen	Spleen
8	chr12:48358200-48360200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:48358200-48360800	Weak transcription	Aorta	Aorta
10	chr12:48358200-48363200	Weak transcription	Brain Substantia Nigra	brain
11	chr12:48358200-48364200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:48358200-48366200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48358200-48366200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:48358400-48359600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:48358400-48359600	Weak transcription	Thymus	Thymus
16	chr12:48358400-48359800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:48358400-48359800	Weak transcription	Fetal Stomach	stomach
18	chr12:48358400-48360200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:48358400-48360600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr12:48358400-48360800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:48358400-48360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:48358400-48361000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:48358400-48361000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:48358400-48361000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:48358400-48361000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:48358400-48361000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:48358400-48361000	Weak transcription	Liver	Liver
28	chr12:48358400-48361000	Weak transcription	Lung	lung
29	chr12:48358400-48361400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:48358400-48362000	Weak transcription	Esophagus	oesophagus
31	chr12:48358400-48362400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:48358400-48362400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:48358400-48362400	Weak transcription	Psoas Muscle	Psoas
34	chr12:48358400-48362800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:48358400-48362800	Weak transcription	NH-A	brain
36	chr12:48358400-48364600	Weak transcription	Ovary	ovary
37	chr12:48358400-48365000	Weak transcription	Osteobl	bone
38	chr12:48358400-48365200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:48358400-48366400	Weak transcription	Fetal Brain Male	brain
40	chr12:48358400-48367800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:48358400-48367800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:48358400-48369800	Weak transcription	Brain Angular Gyrus	brain
43	chr12:48358400-48373000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:48358600-48359600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr12:48358600-48359600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:48358600-48359600	Weak transcription	Right Ventricle	heart
47	chr12:48358600-48359600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:48358600-48360000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:48358600-48360000	Strong transcription	Rectal Smooth Muscle	rectum
50	chr12:48358600-48360000	Weak transcription	NHDF-Ad	bronchial

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