Variant report

Variant	rs6048759
Chromosome Location	chr20:23342361-23342362
allele	A/G
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	chr20:23342202-23342593	GM12892	blood:	n/a	n/a
2	ELK1	chr20:23342265-23342993	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr20:23342240-23342390	GM12865	blood:	n/a	n/a
4	CREB1	chr20:23342304-23342837	ECC-1	luminal epithelium:	n/a	n/a
5	SP1	chr20:23342110-23343043	GM12878	blood:	n/a	chr20:23342747-23342756 chr20:23342529-23342539 chr20:23342530-23342539 chr20:23342748-23342757 chr20:23342528-23342540 chr20:23342188-23342200 chr20:23342529-23342538 chr20:23342529-23342539 chr20:23342797-23342807 chr20:23342529-23342543 chr20:23342529-23342538 chr20:23342528-23342540
6	REST	chr20:23342243-23342566	Hela-S3	cervix:	n/a	n/a
7	GABPA	chr20:23342095-23342758	A549	lung:	n/a	chr20:23342575-23342589 chr20:23342530-23342539 chr20:23342575-23342586 chr20:23342575-23342584 chr20:23342572-23342586
8	TAF1	chr20:23342048-23343519	HepG2	liver:	n/a	n/a
9	HEY1	chr20:23341614-23343339	HepG2	liver:	n/a	chr20:23342230-23342245 chr20:23342846-23342861 chr20:23342852-23342867
10	SIN3AK20	chr20:23341477-23343789	MCF-7	breast:	n/a	n/a
11	NFATC1	chr20:23342298-23342704	GM12878	blood:	n/a	n/a
12	ATF3	chr20:23342200-23342854	A549	lung:	n/a	chr20:23342531-23342551 chr20:23342530-23342539 chr20:23342229-23342238 chr20:23342507-23342516
13	TCF7L2	chr20:23342090-23342821	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr20:23341578-23343854	HepG2	liver:	n/a	n/a
15	CTCF	chr20:23342220-23342370	SAEC	small airway:	n/a	n/a
16	IRF1	chr20:23342342-23342904	K562	blood:	n/a	chr20:23342478-23342489 chr20:23342526-23342540
17	JUND	chr20:23342216-23342960	H1-hESC	embryonic stem cell:	n/a	chr20:23342531-23342540 chr20:23342912-23342921 chr20:23342465-23342479
18	MYC	chr20:23342316-23342709	MCF-7	breast:	n/a	chr20:23342507-23342516 chr20:23342510-23342518
19	CTCF	chr20:23342200-23342470	HCPEpiC	choroid plexus:	n/a	n/a
20	NFATC1	chr20:23342119-23342634	GM12878	blood:	n/a	n/a
21	TAF1	chr20:23342229-23342601	GM12891	blood:	n/a	n/a
22	ZBTB33	chr20:23342235-23342739	A549	lung:	n/a	n/a
23	POLR2A	chr20:23342072-23342725	U87	brain:	n/a	n/a
24	POLR2A	chr20:23341767-23343358	HUVEC	blood vessel:	n/a	n/a
25	PML	chr20:23342105-23342896	MCF-7	breast:	n/a	n/a
26	CTCF	chr20:23342300-23342450	GM12878	blood:	n/a	n/a
27	PAX5	chr20:23341997-23342828	GM12878	blood:	n/a	chr20:23342300-23342310
28	TEAD4	chr20:23342134-23342804	HepG2	liver:	n/a	n/a
29	CEBPB	chr20:23342317-23342919	ECC-1	luminal epithelium:	n/a	chr20:23342621-23342632
30	CHD2	chr20:23341879-23343071	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr20:23342118-23343224	GM10847	blood:	n/a	n/a
32	MYC	chr20:23342015-23342953	Hela-S3	cervix:	n/a	chr20:23342507-23342516 chr20:23342510-23342518 chr20:23342189-23342199
33	REST	chr20:23341663-23343881	H1-neurons	neurons:	n/a	chr20:23342152-23342165 chr20:23342981-23342994 chr20:23343187-23343196 chr20:23343180-23343193 chr20:23342841-23342850 chr20:23342155-23342168
34	ZNF384	chr20:23342324-23342773	K562	blood:	n/a	n/a
35	TAF1	chr20:23342311-23342538	A549	lung:	n/a	n/a
36	REST	chr20:23342350-23342561	GM12878	blood:	n/a	n/a
37	USF1	chr20:23342239-23342724	K562	blood:	n/a	chr20:23342506-23342515 chr20:23342508-23342517 chr20:23342501-23342522 chr20:23342507-23342516 chr20:23342505-23342518 chr20:23342507-23342516 chr20:23342406-23342422
38	SIN3AK20	chr20:23342187-23343163	K562	blood:	n/a	n/a
39	YY1	chr20:23342179-23342823	GM12878	blood:	n/a	chr20:23342804-23342818 chr20:23342779-23342793 chr20:23342530-23342539
40	EP300	chr20:23342273-23342708	GM12878	blood:	n/a	chr20:23342411-23342427
41	YY1	chr20:23342195-23342599	K562	blood:	n/a	chr20:23342530-23342539
42	GTF2F1	chr20:23342232-23342598	K562	blood:	n/a	n/a
43	ATF3	chr20:23342100-23342845	HCT-116	colon:	n/a	chr20:23342531-23342551 chr20:23342530-23342539 chr20:23342229-23342238 chr20:23342507-23342516
44	USF1	chr20:23342215-23342837	A549	lung:	n/a	chr20:23342506-23342515 chr20:23342508-23342517 chr20:23342501-23342522 chr20:23342507-23342516 chr20:23342505-23342518 chr20:23342507-23342516 chr20:23342406-23342422
45	POLR2A	chr20:23341698-23343012	HCT-116	colon:	n/a	n/a
46	HA-E2F1	chr20:23341984-23343188	Hela-S3	cervix:	n/a	chr20:23342530-23342539 chr20:23342984-23342994 chr20:23342576-23342585 chr20:23342915-23342924 chr20:23342679-23342688 chr20:23343149-23343161 chr20:23342858-23342868 chr20:23342916-23342926 chr20:23342764-23342773
47	POLR2A	chr20:23342113-23343344	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr20:23341677-23343139	ECC-1	luminal epithelium:	n/a	n/a
49	BCL11A	chr20:23342309-23342537	GM12878	blood:	n/a	n/a
50	TAF1	chr20:23342209-23342507	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:20922188..20924523-chr20:23341669..23343744,2	MCF-7	breast:
2	chr20:23340954..23342681-chr20:23403293..23405458,3	MCF-7	breast:
3	chr20:23340976..23344072-chr20:23400128..23403114,5	K562	blood:
4	chr20:23342068..23342615-chr6:16129171..16129844,2	HCT-116	colon:
5	chr20:23342009..23344759-chr20:23616093..23619702,3	MCF-7	breast:
6	chr19:49303116..49303675-chr20:23341504..23342477,2	Hela-S3	cervix:
7	chr12:112856133..112856816-chr20:23342324..23343158,2	NB4	blood:
8	chr17:56735124..56736858-chr20:23339891..23342718,2	MCF-7	breast:
9	chr20:23341938..23342938-chr7:44613359..44613870,2	HCT-116	colon:
10	chr20:23337918..23344174-chr20:23400107..23404916,9	MCF-7	breast:
11	chr12:7052555..7053156-chr20:23342059..23342617,2	NB4	blood:
12	chr15:71407056..71408775-chr20:23342043..23343755,2	MCF-7	breast:
13	chr20:23340884..23343229-chr20:23616953..23618725,2	K562	blood:
14	chr11:61735662..61736427-chr20:23341928..23342453,2	Hela-S3	cervix:
15	chr20:23342007..23342541-chr6:30457292..30457800,2	NB4	blood:
16	chr20:23339750..23342379-chr20:23399207..23403196,4	MCF-7	breast:
17	chr20:23342090..23342675-chr20:42218497..42219055,2	Hela-S3	cervix:
18	chr20:23338809..23345308-chr20:23399768..23403114,12	K562	blood:
19	chr1:206808253..206808855-chr20:23342165..23342721,2	NB4	blood:

Variant related genes	Relation type
GZF1	TF binding region
ENSG00000232645	TF binding region
ENSG00000111678	Chromatin interaction
ENSG00000089009	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000092094	Chromatin interaction
ENSG00000125814	Chromatin interaction
ENSG00000100823	Chromatin interaction
ENSG00000136271	Chromatin interaction
ENSG00000179295	Chromatin interaction
ENSG00000007944	Chromatin interaction
ENSG00000225362	Chromatin interaction
ENSG00000101439	Chromatin interaction

Extended variants
information (count: 1 )
Associated
traits (count: 0)

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	esv3338336	chr20:23341577-23344125	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23341200-23342400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr20:23341200-23343600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr20:23341400-23342400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr20:23341400-23342400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:23341400-23342400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr20:23341400-23342400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr20:23341400-23343800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr20:23341600-23342400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr20:23341600-23342400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr20:23341600-23342400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr20:23341600-23342400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr20:23341600-23342400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr20:23341600-23342400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr20:23341600-23343600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr20:23341600-23343800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr20:23341600-23343800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr20:23341800-23342400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr20:23341800-23342400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr20:23341800-23342400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:23341800-23342400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr20:23341800-23342400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr20:23341800-23342800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr20:23341800-23343200	Active TSS	Fetal Muscle Trunk	muscle
24	chr20:23341800-23343400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:23341800-23343400	Active TSS	Colonic Mucosa	Colon
26	chr20:23341800-23343400	Active TSS	Fetal Brain Female	brain
27	chr20:23341800-23343400	Active TSS	Right Ventricle	heart
28	chr20:23341800-23343600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr20:23341800-23343600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr20:23341800-23343600	Active TSS	Ovary	ovary
31	chr20:23341800-23343600	Active TSS	Psoas Muscle	Psoas
32	chr20:23341800-23343800	Active TSS	Lung	lung
33	chr20:23342000-23342400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr20:23342000-23342400	Active TSS	Fetal Heart	heart
35	chr20:23342000-23343200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr20:23342000-23343200	Active TSS	Placenta	Placenta
37	chr20:23342000-23343400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr20:23342000-23343400	Active TSS	Primary T cells from cord blood	blood
39	chr20:23342000-23343400	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr20:23342000-23343400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr20:23342000-23343400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr20:23342000-23343400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr20:23342000-23343400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr20:23342000-23343400	Active TSS	Liver	Liver
45	chr20:23342000-23343400	Active TSS	Brain Anterior Caudate	brain
46	chr20:23342000-23343400	Active TSS	Brain Cingulate Gyrus	brain
47	chr20:23342000-23343400	Active TSS	Brain Germinal Matrix	brain
48	chr20:23342000-23343400	Active TSS	Brain Hippocampus Middle	brain
49	chr20:23342000-23343400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr20:23342000-23343400	Active TSS	Brain Substantia Nigra	brain

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