Variant report

Variant	rs73428502
Chromosome Location	chr11:18814300-18814301
allele	G/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	MAX	chr11:18813633-18814334	H1-hESC	embryonic stem cell:	n/a	chr11:18813989-18813999
2	SIN3A	chr11:18812490-18814369	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:18812402-18814321	H1-neurons	neurons:	n/a	n/a
4	REST	chr11:18812198-18814425	H1-neurons	neurons:	n/a	chr11:18813614-18813627 chr11:18812751-18812764 chr11:18813049-18813062 chr11:18814081-18814091
5	MAX	chr11:18813652-18814304	H1-hESC	embryonic stem cell:	n/a	chr11:18813989-18813999

Variant related genes	Relation type
PTPN5	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11024796	0.95[ASN][1000 genomes]
rs11024798	0.86[ASN][1000 genomes]
rs12223440	0.86[ASN][1000 genomes]
rs12576955	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4277090	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4539305	0.86[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	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73428502	PTPN5	cis	lung	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18812200-18814600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr11:18812400-18814400	Active TSS	Brain Angular Gyrus	brain
3	chr11:18812400-18814600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr11:18812400-18814600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr11:18812400-18814600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr11:18812400-18814600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr11:18812600-18814600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr11:18812800-18814400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:18812800-18814400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:18813800-18814400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:18813800-18814400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:18813800-18814400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
13	chr11:18813800-18814400	Bivalent Enhancer	Ovary	ovary
14	chr11:18813800-18814400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
15	chr11:18813800-18814600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr11:18813800-18814600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:18813800-18814600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
18	chr11:18814000-18814400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr11:18814000-18814400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:18814000-18814600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr11:18814000-18814600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
22	chr11:18814200-18814400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:18814200-18814400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:18814200-18814400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:18814200-18814400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:18814200-18814400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
27	chr11:18814200-18814400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:18814200-18814400	Bivalent Enhancer	Fetal Brain Male	brain
29	chr11:18814200-18814400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
30	chr11:18814200-18814400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr11:18814200-18814600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:18814200-18814600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell

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