Variant report

Variant	rs12932212
Chromosome Location	chr16:79675253-79675254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:79672405..79675476-chr16:79684615..79687240,3	MCF-7	breast:
2	chr16:79669312..79671959-chr16:79673803..79675378,2	K562	blood:
3	chr16:79673720..79676616-chr16:79676975..79679637,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10514466	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11150182	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11150185	0.84[EUR][1000 genomes]
rs11150186	0.87[CEU][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12935094	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1424235	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4889005	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4889006	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6564685	0.88[EUR][1000 genomes]
rs7204271	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8043576	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8055105	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv833295	chr16:79568878-79726768	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv906992	chr16:79649394-79769790	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12932212	GAN	cis	cerebellum	SCAN
rs12932212	ZNRF1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79666400-79682200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:79673400-79675400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
3	chr16:79673400-79675400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:79673400-79676400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr16:79673600-79675400	Enhancers	Fetal Muscle Leg	muscle
6	chr16:79673600-79677200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:79674000-79675600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr16:79674400-79675400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr16:79674400-79675400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr16:79674400-79675800	Enhancers	Fetal Stomach	stomach
11	chr16:79674400-79686400	Weak transcription	Fetal Thymus	thymus
12	chr16:79674600-79675400	Enhancers	NHLF	lung
13	chr16:79674800-79675400	Enhancers	Duodenum Mucosa	Duodenum
14	chr16:79674800-79676800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr16:79674800-79681600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr16:79675000-79675400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
17	chr16:79675000-79675400	Enhancers	NHEK	skin
18	chr16:79675000-79675600	Enhancers	Primary T cells from cord blood	blood
19	chr16:79675000-79675600	Enhancers	Fetal Lung	lung
20	chr16:79675000-79675800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr16:79675000-79677200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr16:79675000-79678200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:79675000-79678400	Weak transcription	HMEC	breast
24	chr16:79675200-79675400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr16:79675200-79675400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:79675200-79675400	Enhancers	Brain Germinal Matrix	brain
27	chr16:79675200-79675400	Enhancers	Fetal Kidney	kidney
28	chr16:79675200-79675600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr16:79675200-79675600	Enhancers	HSMMtube	muscle
30	chr16:79675200-79677000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr16:79675200-79677000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr16:79675200-79677800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr16:79675200-79678600	Weak transcription	HSMM	muscle
34	chr16:79675200-79679000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr16:79675200-79679200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr16:79675200-79679200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr16:79675200-79679400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr16:79675200-79685200	Weak transcription	Fetal Muscle Trunk	muscle

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