Variant report

Variant	rs570500669
Chromosome Location	chr20:41818942-41818943
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr20:41818886-41818975	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr20:41818934-41819178	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr20:41818609-41819065	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr20:41818335-41819058	H1-neurons	neurons:	n/a	n/a
5	CTCF	chr20:41818807-41818948	H1-hESC	embryonic stem cell:	n/a	n/a
6	BACH1	chr20:41818772-41819165	H1-hESC	embryonic stem cell:	n/a	n/a
7	EGR1	chr20:41818658-41819065	H1-hESC	embryonic stem cell:	n/a	chr20:41818792-41818814 chr20:41819041-41819051 chr20:41818893-41818902 chr20:41818798-41818807
8	SUZ12	chr20:41816560-41819205	NT2-D1	testis:	n/a	n/a
9	EGR1	chr20:41818791-41818994	K562	blood:	n/a	chr20:41818792-41818814 chr20:41818893-41818902 chr20:41818798-41818807

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:41818905-41818955	GM06990	blood:	n/a
2	chr20:41818905-41818955	NHBE	bronchial:	n/a
3	chr20:41818905-41818955	MCF-7	breast:	n/a
4	chr20:41818905-41818955	ECC-1	luminal epithelium:	n/a
5	chr20:41818905-41818955	AG04450	lung:	fetal
6	chr20:41818905-41818955	HAEpiC	amniotic membrane:	n/a
7	chr20:41818905-41818955	HPAEpiC	pulmonary alveolar:	n/a
8	chr20:41818905-41818955	Jurkat	blood:	n/a
9	chr20:41818905-41818955	GM19239	blood:	n/a
10	chr20:41818905-41818955	Hela-S3	cervix:	n/a
11	chr20:41818905-41818955	U87	brain:	n/a
12	chr20:41818905-41818955	HRE	kidney:	n/a
13	chr20:41818905-41818955	NB4	blood:	n/a
14	chr20:41818905-41818955	HRCEpiC	kidney:	n/a
15	chr20:41818905-41818955	Hepatocyte	liver:	n/a
16	chr20:41818905-41818955	HUVEC	blood vessel:	n/a
17	chr20:41818905-41818955	HCPEpiC	choroid plexus:	n/a
18	chr20:41818905-41818955	AG04449	skin:	fetal
19	chr20:41818905-41818955	GM12891	blood:	n/a
20	chr20:41818905-41818955	ovcar-3	ovarian:	n/a
21	chr20:41818905-41818955	HEK293	kidney:	embryo
22	chr20:41818905-41818955	Caco-2	colon:	n/a
23	chr20:41818905-41818955	GM12878	blood:	n/a
24	chr20:41818905-41818955	RPTEC	kidney:	n/a
25	chr20:41818905-41818955	BE2_C	brain:	n/a
26	chr20:41818905-41818955	CMK	blood:	n/a
27	chr20:41818905-41818955	IMR90	lung:	fetal
28	chr20:41818905-41818955	HEEpiC	esophagus:	n/a
29	chr20:41818905-41818955	PFSK-1	brain:	n/a
30	chr20:41818905-41818955	HCM	heart:	n/a
31	chr20:41818905-41818955	NHDF-neo	bronchial:	n/a
32	chr20:41818905-41818955	SK-N-SH	brain:	n/a
33	chr20:41818905-41818955	K562	blood:	n/a
34	chr20:41818905-41818955	NH-A	brain:	n/a
35	chr20:41818905-41818955	NT2-D1	testis:	n/a
36	chr20:41818905-41818955	SAEC	small airway:	n/a
37	chr20:41818905-41818955	HMEC	breast:	n/a
38	chr20:41818905-41818955	SK-N-SH_RA	brain:	n/a
39	chr20:41818905-41818955	PANC-1	pancreas:	n/a
40	chr20:41818905-41818955	ProgFib	skin:	n/a
41	chr20:41818905-41818955	AoSMC	blood vessel:	n/a
42	chr20:41818905-41818955	PrEC	prostate:	n/a
43	chr20:41818905-41818955	AG09309	skin:	n/a
44	chr20:41818905-41818955	MCF10A-Er-Src	breast:	n/a
45	chr20:41818905-41818955	GM12892	blood:	n/a
46	chr20:41818905-41818955	HRPEpiC	eye:	n/a
47	chr20:41818905-41818955	HCT-116	colon:	n/a
48	chr20:41818905-41818955	H1-hESC	embryonic stem cell:	embryo
49	chr20:41818905-41818955	AG10803	skin:	n/a
50	chr20:41818905-41818955	HIPEpiC	eye:	n/a

No data

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

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2751914	chr20:41744586-41890453	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3412564	chr20:41817238-41820486	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3329299	chr20:41817363-41819911	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41815400-41819000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr20:41816600-41819000	Enhancers	Pancreas	Pancrea
3	chr20:41816600-41819200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:41816600-41819400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr20:41816600-41819400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr20:41817000-41819400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr20:41817000-41819400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr20:41817000-41819400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr20:41817200-41819000	Bivalent/Poised TSS	Right Ventricle	heart
10	chr20:41817200-41819200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr20:41817200-41819200	Active TSS	Brain Angular Gyrus	brain
12	chr20:41817200-41819400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr20:41817200-41819400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr20:41817200-41819400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
15	chr20:41817200-41819800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr20:41817400-41819000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr20:41817600-41819000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr20:41817600-41819000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr20:41817600-41820000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr20:41817800-41819000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:41818000-41819000	Bivalent/Poised TSS	Psoas Muscle	Psoas
22	chr20:41818000-41819200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr20:41818200-41819000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr20:41818200-41819000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
25	chr20:41818200-41819000	Bivalent/Poised TSS	Fetal Brain Female	brain
26	chr20:41818600-41819000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr20:41818600-41819000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr20:41818600-41819000	Bivalent Enhancer	Fetal Brain Male	brain
29	chr20:41818600-41819000	Bivalent Enhancer	Spleen	Spleen
30	chr20:41818800-41819000	Bivalent Enhancer	Adipose Nuclei	Adipose
31	chr20:41818800-41819000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
32	chr20:41818800-41819000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr20:41818800-41819000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr20:41818800-41819000	Bivalent Enhancer	Fetal Lung	lung
35	chr20:41818800-41819000	Bivalent/Poised TSS	Fetal Stomach	stomach
36	chr20:41818800-41819000	Bivalent Enhancer	Left Ventricle	heart
37	chr20:41818800-41819000	Bivalent Enhancer	Lung	lung
38	chr20:41818800-41819000	Bivalent Enhancer	Right Atrium	heart
39	chr20:41818800-41819000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
40	chr20:41818800-41819200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr20:41818800-41819200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
42	chr20:41818800-41819400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
43	chr20:41818800-41819400	Active TSS	Brain Anterior Caudate	brain
44	chr20:41818800-41819600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr20:41818800-41819600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
46	chr20:41818800-41821200	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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