Variant report

Variant	rs2060132
Chromosome Location	chr9:116938911-116938912
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116938018..116940765-chr9:116944712..116947136,2	K562	blood:
2	chr9:116938315..116939926-chr9:116941668..116944207,2	MCF-7	breast:
3	chr9:116927944..116931145-chr9:116936589..116939261,3	MCF-7	breast:
4	chr9:116918121..116920168-chr9:116937255..116940070,3	K562	blood:
5	chr9:116936810..116939518-chr9:116945636..116948871,3	K562	blood:
6	chr9:116932183..116936074-chr9:116938591..116942808,3	K562	blood:

Variant related genes	Relation type
ENSG00000196739	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1431819	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2567707	0.82[MEX][hapmap]
rs4978571	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4979347	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4979349	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7855790	0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
5	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
6	nsv893752	chr9:116899258-116944333	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv466531	chr9:116916931-116940418	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv615231	chr9:116916931-116940418	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv466532	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv615232	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv466533	chr9:116930100-117248479	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
12	nsv615233	chr9:116930100-117248479	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
13	esv2761551	chr9:116935526-116940489	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2060132	ZNF483	cis	cerebellum	SCAN
rs2060132	COL27A1,MIR455	cis	hippocampus	BrainEAC

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116919200-116972000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:116919600-116939600	Weak transcription	Hela-S3	cervix
3	chr9:116926200-116943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:116926400-116950200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:116926400-116950400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:116926600-116939400	Weak transcription	Fetal Kidney	kidney
7	chr9:116930600-116954400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:116931000-116946400	Genic enhancers	Fetal Stomach	stomach
9	chr9:116931000-116971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:116932800-116939200	Weak transcription	Osteobl	bone
11	chr9:116932800-116943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:116932800-116971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:116933000-116939400	Weak transcription	Fetal Lung	lung
14	chr9:116933200-116939000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:116933200-116939200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:116933200-116940400	Weak transcription	Spleen	Spleen
17	chr9:116934400-116940600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr9:116934400-116942800	Enhancers	Colon Smooth Muscle	Colon
19	chr9:116934600-116940600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:116934800-116940000	Enhancers	Stomach Smooth Muscle	stomach
21	chr9:116934800-116942000	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:116935000-116946600	Enhancers	Liver	Liver
23	chr9:116935200-116940800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:116935200-116941600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:116935200-116942000	Enhancers	Pancreas	Pancrea
26	chr9:116935200-116944800	Enhancers	Fetal Heart	heart
27	chr9:116935200-116944800	Enhancers	Left Ventricle	heart
28	chr9:116935200-116945400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr9:116935400-116940000	Enhancers	Fetal Intestine Large	intestine
30	chr9:116935600-116939000	Weak transcription	Ovary	ovary
31	chr9:116935800-116939000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:116935800-116939200	Weak transcription	Adipose Nuclei	Adipose
33	chr9:116935800-116939400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:116936000-116939000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:116936000-116939400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:116936000-116939600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:116936000-116940000	Enhancers	Fetal Muscle Trunk	muscle
38	chr9:116936200-116939400	Weak transcription	HMEC	breast
39	chr9:116936200-116939600	Weak transcription	Esophagus	oesophagus
40	chr9:116936400-116944400	Enhancers	Placenta	Placenta
41	chr9:116936600-116939200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr9:116936600-116940400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr9:116936600-116941000	Enhancers	NH-A	brain
44	chr9:116936600-116941800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:116936600-116941800	Enhancers	Psoas Muscle	Psoas
46	chr9:116936800-116939600	Enhancers	Brain Angular Gyrus	brain
47	chr9:116937000-116940000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:116937200-116940000	Enhancers	NHLF	lung
49	chr9:116937200-116941200	Enhancers	HSMMtube	muscle
50	chr9:116937400-116939000	Strong transcription	NHEK	skin

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