Variant report

Variant	rs4277090
Chromosome Location	chr11:18813489-18813490
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:183)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:18812922-18813622	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr11:18812959-18813871	H1-neurons	neurons:	n/a	chr11:18813614-18813627 chr11:18813049-18813062
3	TAF1	chr11:18812861-18813491	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr11:18813135-18813587	H1-hESC	embryonic stem cell:	n/a	chr11:18813444-18813453
5	MAX	chr11:18812842-18813536	H1-hESC	embryonic stem cell:	n/a	chr11:18813012-18813022 chr11:18812872-18812882
6	POLR2A	chr11:18812431-18813935	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr11:18812880-18813513	H1-hESC	embryonic stem cell:	n/a	chr11:18813352-18813362 chr11:18813043-18813050
8	CTBP2	chr11:18812602-18814242	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr11:18812490-18814369	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr11:18812715-18813630	H1-hESC	embryonic stem cell:	n/a	chr11:18813352-18813362 chr11:18813043-18813050
11	EGR1	chr11:18812696-18813602	H1-hESC	embryonic stem cell:	n/a	chr11:18813223-18813237 chr11:18813290-18813299 chr11:18813013-18813023
12	POLR2A	chr11:18812402-18814321	H1-neurons	neurons:	n/a	n/a
13	REST	chr11:18812198-18814425	H1-neurons	neurons:	n/a	chr11:18813614-18813627 chr11:18812751-18812764 chr11:18813049-18813062 chr11:18814081-18814091
14	POLR2A	chr11:18812552-18813731	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr11:18812635-18814298	H1-neurons	neurons:	n/a	n/a
16	TAF1	chr11:18812861-18813544	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr11:18812449-18814279	H1-neurons	neurons:	n/a	n/a
18	TAF1	chr11:18812968-18814013	H1-neurons	neurons:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:18813484-18813534	AG04449	skin:	fetal
2	chr11:18813484-18813534	Jurkat	blood:	n/a
3	chr11:18813484-18813534	NHBE	bronchial:	n/a
4	chr11:18813484-18813534	HCT-116	colon:	n/a
5	chr11:18813484-18813534	PrEC	prostate:	n/a
6	chr11:18813477-18813527	GM06990	blood:	n/a
7	chr11:18813484-18813534	AG09309	skin:	n/a
8	chr11:18813477-18813527	HCT-116	colon:	n/a
9	chr11:18813477-18813527	NH-A	brain:	n/a
10	chr11:18813477-18813527	Hela-S3	cervix:	n/a
11	chr11:18813466-18813516	SK-N-MC	brain:	n/a
12	chr11:18813477-18813527	HPAEpiC	pulmonary alveolar:	n/a
13	chr11:18813466-18813516	AG04449	skin:	fetal
14	chr11:18813477-18813527	SK-N-SH	brain:	n/a
15	chr11:18813484-18813534	HUVEC	blood vessel:	n/a
16	chr11:18813484-18813534	MCF10A-Er-Src	breast:	n/a
17	chr11:18813484-18813534	BE2_C	brain:	n/a
18	chr11:18813477-18813527	PANC-1	pancreas:	n/a
19	chr11:18813477-18813527	AG04450	lung:	fetal
20	chr11:18813484-18813534	HNPCEpiC	eye:	n/a
21	chr11:18813466-18813516	SAEC	small airway:	n/a
22	chr11:18813477-18813527	HMEC	breast:	n/a
23	chr11:18813466-18813516	MCF10A-Er-Src	breast:	n/a
24	chr11:18813484-18813534	K562	blood:	n/a
25	chr11:18813466-18813516	SKMC	muscle:	n/a
26	chr11:18813466-18813516	HCPEpiC	choroid plexus:	n/a
27	chr11:18813477-18813527	HNPCEpiC	eye:	n/a
28	chr11:18813477-18813527	SK-N-SH_RA	brain:	n/a
29	chr11:18813484-18813534	HCPEpiC	choroid plexus:	n/a
30	chr11:18813477-18813527	ProgFib	skin:	n/a
31	chr11:18813466-18813516	NB4	blood:	n/a
32	chr11:18813466-18813516	PrEC	prostate:	n/a
33	chr11:18813484-18813534	MCF-7	breast:	n/a
34	chr11:18813466-18813516	Hepatocyte	liver:	n/a
35	chr11:18813484-18813534	IMR90	lung:	fetal
36	chr11:18813477-18813527	HRCEpiC	kidney:	n/a
37	chr11:18813477-18813527	HRPEpiC	eye:	n/a
38	chr11:18813484-18813534	GM12891	blood:	n/a
39	chr11:18813484-18813534	ovcar-3	ovarian:	n/a
40	chr11:18813477-18813527	AG10803	skin:	n/a
41	chr11:18813466-18813516	NT2-D1	testis:	n/a
42	chr11:18813484-18813534	HAEpiC	amniotic membrane:	n/a
43	chr11:18813477-18813527	PrEC	prostate:	n/a
44	chr11:18813466-18813516	HUVEC	blood vessel:	n/a
45	chr11:18813466-18813516	MCF-7	breast:	n/a
46	chr11:18813477-18813527	HCF	heart:	n/a
47	chr11:18813477-18813527	HEEpiC	esophagus:	n/a
48	chr11:18813466-18813516	HepG2	liver:	n/a
49	chr11:18813477-18813527	HL-60	blood:	n/a
50	chr11:18813484-18813534	CMK	blood:	n/a

No data

Variant related genes	Relation type
PTPN5	TF binding region
PTPN5	CpG island

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	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4539305	0.86[ASN][1000 genomes]
rs73428502	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs4277090	PTPN5	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18811400-18813600	Active TSS	Brain Anterior Caudate	brain
2	chr11:18811800-18813600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:18811800-18813800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr11:18812200-18814000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
5	chr11:18812200-18814200	Bivalent/Poised TSS	Fetal Brain Female	brain
6	chr11:18812200-18814600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr11:18812400-18813800	Active TSS	Fetal Brain Male	brain
8	chr11:18812400-18813800	Active TSS	Right Atrium	heart
9	chr11:18812400-18814000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:18812400-18814200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:18812400-18814200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr11:18812400-18814400	Active TSS	Brain Angular Gyrus	brain
13	chr11:18812400-18814600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr11:18812400-18814600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr11:18812400-18814600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr11:18812400-18814600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr11:18812600-18813600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr11:18812600-18813600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:18812600-18813600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:18812600-18813800	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr11:18812600-18813800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:18812600-18813800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
23	chr11:18812600-18813800	Bivalent/Poised TSS	A549	lung
24	chr11:18812600-18814000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr11:18812600-18814000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:18812600-18814000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:18812600-18814000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
28	chr11:18812600-18814000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
29	chr11:18812600-18814200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:18812600-18814200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:18812600-18814200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:18812600-18814200	Bivalent Enhancer	Liver	Liver
33	chr11:18812600-18814200	Bivalent Enhancer	Placenta	Placenta
34	chr11:18812600-18814600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr11:18812800-18813600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:18812800-18813600	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr11:18812800-18813600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
38	chr11:18812800-18813600	Bivalent/Poised TSS	Fetal Stomach	stomach
39	chr11:18812800-18813600	Active TSS	Psoas Muscle	Psoas
40	chr11:18812800-18813600	Bivalent/Poised TSS	HSMMtube	muscle
41	chr11:18812800-18813600	Bivalent/Poised TSS	NH-A	brain
42	chr11:18812800-18813800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:18812800-18813800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
44	chr11:18812800-18813800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:18812800-18813800	Bivalent Enhancer	Spleen	Spleen
46	chr11:18812800-18814000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:18812800-18814000	Bivalent Enhancer	Fetal Heart	heart
48	chr11:18812800-18814400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:18812800-18814400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:18813000-18813600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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