Variant report

Variant	rs28479912
Chromosome Location	chr19:39444139-39444140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39442317-39445459	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
FBXO17	TF binding region
SARS2	TF binding region
ENSG00000269547	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12974911	0.80[AFR][1000 genomes]
rs34195234	0.82[AFR][1000 genomes]
rs7246128	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248334	0.90[EUR][1000 genomes]
rs7249553	0.90[EUR][1000 genomes];0.92[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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28479912	FBXO27	cis	Esophagus Mucosa	GTEx
rs28479912	CTB-189B5.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
2	chr19:39435800-39453000	Weak transcription	K562	blood
3	chr19:39438200-39447000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:39438400-39453000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr19:39439200-39452600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:39439600-39446200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:39441000-39444400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:39441000-39453000	Weak transcription	Aorta	Aorta
9	chr19:39441000-39459200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:39441200-39446400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:39441200-39447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:39441200-39448200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:39441200-39449200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:39441200-39449200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr19:39441200-39450400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:39441200-39452800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:39441200-39453000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:39441200-39453000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:39441200-39453000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:39441200-39453000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:39441200-39453000	Weak transcription	Brain Hippocampus Middle	brain
22	chr19:39441200-39453000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:39441200-39453000	Weak transcription	Lung	lung
24	chr19:39441200-39453000	Weak transcription	Pancreas	Pancrea
25	chr19:39441200-39453000	Weak transcription	Osteobl	bone
26	chr19:39441200-39455800	Weak transcription	Psoas Muscle	Psoas
27	chr19:39441200-39459400	Weak transcription	Fetal Lung	lung
28	chr19:39441200-39465200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr19:39441200-39465200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:39441200-39465200	Weak transcription	NHLF	lung
31	chr19:39441200-39465400	Weak transcription	Right Atrium	heart
32	chr19:39441400-39444200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr19:39441400-39445800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:39441400-39447600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:39441400-39447600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr19:39441400-39452600	Weak transcription	Adipose Nuclei	Adipose
37	chr19:39441400-39452600	Weak transcription	Colon Smooth Muscle	Colon
38	chr19:39441400-39453000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:39441400-39453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:39441400-39453000	Weak transcription	Fetal Brain Male	brain
41	chr19:39441400-39453000	Weak transcription	Fetal Brain Female	brain
42	chr19:39441400-39453000	Weak transcription	Ovary	ovary
43	chr19:39441400-39453000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr19:39441400-39453200	Weak transcription	Fetal Heart	heart
45	chr19:39441400-39462000	Weak transcription	Small Intestine	intestine
46	chr19:39441400-39465000	Weak transcription	HUVEC	blood vessel
47	chr19:39441600-39450200	Strong transcription	Fetal Stomach	stomach
48	chr19:39441800-39444800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr19:39442400-39445000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:39442800-39444800	Enhancers	HepG2	liver

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