Variant report

Variant	rs4979289
Chromosome Location	chr9:116654624-116654625
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	chr9:116651215..116653821-chr9:116654616..116657370,3	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12551599	0.87[AMR][1000 genomes]
rs13285566	1.00[CEU][hapmap]
rs13301669	1.00[CEU][hapmap]
rs17200294	0.95[CEU][hapmap]
rs17200714	1.00[CEU][hapmap]
rs1999203	0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4979290	1.00[CEU][hapmap]
rs7040810	0.95[CEU][hapmap]
rs7041034	0.95[CEU][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4979289	C7orf20	trans	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116639200-116663400	Weak transcription	Gastric	stomach
2	chr9:116649200-116658000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:116649600-116660000	Weak transcription	Small Intestine	intestine
4	chr9:116649800-116655000	Weak transcription	Stomach Mucosa	stomach
5	chr9:116649800-116663800	Weak transcription	HSMMtube	muscle
6	chr9:116649800-116668600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:116650200-116657600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:116650200-116657800	Weak transcription	HUVEC	blood vessel
9	chr9:116650600-116662800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr9:116651000-116654800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:116651000-116662600	Weak transcription	Fetal Intestine Small	intestine
12	chr9:116651000-116662800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:116651000-116668000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:116651200-116663200	Weak transcription	Fetal Stomach	stomach
15	chr9:116651200-116675000	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:116651600-116655400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:116651800-116655400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr9:116652000-116655200	Weak transcription	Pancreas	Pancrea
19	chr9:116652200-116655200	Weak transcription	Ovary	ovary
20	chr9:116652200-116668400	Weak transcription	NH-A	brain
21	chr9:116653000-116657800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:116653000-116657800	Weak transcription	K562	blood
23	chr9:116653000-116663800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:116653200-116655200	Weak transcription	A549	lung
25	chr9:116653200-116655400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:116653200-116656800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:116653200-116657200	Weak transcription	Fetal Kidney	kidney
28	chr9:116653200-116658400	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:116653200-116660400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:116653200-116668400	Weak transcription	NHLF	lung
31	chr9:116653200-116669600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:116653200-116671800	Weak transcription	Fetal Lung	lung
33	chr9:116653400-116657800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:116653400-116669000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:116653800-116657400	Weak transcription	NHDF-Ad	bronchial
36	chr9:116653800-116665400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:116653800-116669000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:116653800-116674000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:116654000-116657800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr9:116654000-116661400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:116654200-116658400	Enhancers	Liver	Liver
42	chr9:116654400-116665400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:116654400-116668200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:116654600-116655600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:116654600-116663600	Weak transcription	HSMM	muscle

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