Variant report

Variant	rs56088054
Chromosome Location	chr2:73297743-73297744
allele	A/C
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	TCF12	chr2:73297570-73299220	ECC-1	luminal epithelium:	n/a	n/a
2	E2F6	chr2:73297698-73299262	K562	blood:	n/a	chr2:73298476-73298483 chr2:73298472-73298484 chr2:73298476-73298483 chr2:73298473-73298484 chr2:73298550-73298559 chr2:73298476-73298483
3	RUNX3	chr2:73297459-73297749	GM12878	blood:	n/a	n/a
4	MYC	chr2:73297619-73299075	NB4	blood:	n/a	chr2:73298883-73298893 chr2:73298489-73298499
5	ZNF384	chr2:73296290-73298008	K562	blood:	n/a	n/a
6	CREB1	chr2:73297606-73299152	A549	lung:	n/a	n/a
7	PML	chr2:73297647-73299043	K562	blood:	n/a	n/a
8	HDAC2	chr2:73297699-73299286	HepG2	liver:	n/a	n/a
9	YY1	chr2:73297566-73299169	K562	blood:	n/a	chr2:73298618-73298632 chr2:73298466-73298480 chr2:73298621-73298635
10	POLR2A	chr2:73297693-73299220	U87	brain:	n/a	n/a
11	SIN3AK20	chr2:73297725-73298503	HepG2	liver:	n/a	n/a
12	STAT5A	chr2:73297438-73297772	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:73297442-73299194	Hela-S3	cervix:	n/a	n/a
14	TBL1XR1	chr2:73297672-73297818	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:73297664-73299490	GM12878	blood:	n/a	n/a
16	ZBTB7A	chr2:73297513-73299079	ECC-1	luminal epithelium:	n/a	n/a
17	TAF1	chr2:73297514-73299114	K562	blood:	n/a	n/a
18	EGR1	chr2:73297565-73298275	K562	blood:	n/a	chr2:73297808-73297822
19	EGR1	chr2:73297597-73298004	ECC-1	luminal epithelium:	n/a	chr2:73297808-73297822
20	MTA3	chr2:73297444-73297899	GM12878	blood:	n/a	n/a
21	EGR1	chr2:73297418-73299295	HCT-116	colon:	n/a	chr2:73298794-73298808 chr2:73297808-73297822 chr2:73298941-73298965
22	MAZ	chr2:73297661-73299511	GM12878	blood:	n/a	chr2:73298883-73298893 chr2:73298489-73298499
23	ZBTB7A	chr2:73297523-73299186	K562	blood:	n/a	n/a
24	POLR2A	chr2:73297648-73299556	GM15510	blood:	n/a	n/a
25	POLR2A	chr2:73297638-73299067	Hela-S3	cervix:	n/a	n/a
26	SMARCB1	chr2:73297554-73299419	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr2:73297713-73299674	A549	lung:	n/a	n/a
28	POLR2A	chr2:73297694-73299271	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr2:73297601-73299706	HUVEC	blood vessel:	n/a	n/a
30	MAZ	chr2:73296297-73299255	IMR90	lung:	n/a	chr2:73298883-73298893 chr2:73298489-73298499
31	MAX	chr2:73297643-73299173	MCF-7	breast:	n/a	chr2:73298883-73298893 chr2:73298489-73298499
32	HMGN3	chr2:73297581-73299545	K562	blood:	n/a	n/a
33	POLR2A	chr2:73297597-73299543	GM18505	blood:	n/a	n/a
34	POLR2A	chr2:73297561-73299376	A549	lung:	n/a	n/a
35	POLR2A	chr2:73297218-73299374	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr2:73297472-73299711	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr2:73297693-73299140	HUVEC	blood vessel:	n/a	n/a
38	E2F4	chr2:73297500-73297914	MCF10A-Er-Src	breast:	n/a	n/a
39	E2F6	chr2:73297632-73298644	K562	blood:	n/a	chr2:73298476-73298483 chr2:73298472-73298484 chr2:73298476-73298483 chr2:73298473-73298484 chr2:73298550-73298559 chr2:73298476-73298483
40	CHD2	chr2:73297688-73299108	Hela-S3	cervix:	n/a	n/a
41	TAF1	chr2:73297620-73299485	HepG2	liver:	n/a	n/a
42	MAX	chr2:73297045-73299353	A549	lung:	n/a	chr2:73298883-73298893 chr2:73298489-73298499
43	POLR2A	chr2:73296225-73299135	K562	blood:	n/a	n/a
44	TAF1	chr2:73297598-73297943	H1-hESC	embryonic stem cell:	n/a	n/a
45	HEY1	chr2:73297531-73299036	K562	blood:	n/a	n/a
46	TAF1	chr2:73297668-73299050	K562	blood:	n/a	n/a
47	SIN3AK20	chr2:73297517-73299159	PANC-1	pancreas:	n/a	n/a
48	MAZ	chr2:73296169-73299305	K562	blood:	n/a	chr2:73298883-73298893 chr2:73298489-73298499
49	POLR2A	chr2:73297440-73299428	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr2:73296314-73299380	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:73218132..73222464-chr2:73296356..73300991,4	K562	blood:
2	chr2:71221874..71223413-chr2:73296687..73299396,2	K562	blood:
3	chr2:73296244..73298765-chr2:73460240..73462407,3	MCF-7	breast:
4	chr2:73297299..73299304-chr2:73339003..73341312,3	MCF-7	breast:
5	chr2:73297070..73299155-chr2:73306515..73308628,3	MCF-7	breast:
6	chr2:73296621..73300316-chr2:73309682..73312950,4	K562	blood:
7	chr2:73297623..73300370-chr2:73303769..73308752,6	MCF-7	breast:
8	chr2:73297144..73299999-chr2:73458885..73461387,2	MCF-7	breast:
9	chr2:73296300..73298115-chr2:73338664..73340371,2	K562	blood:
10	chr2:73219221..73222584-chr2:73297203..73300121,3	MCF-7	breast:
11	chr2:73284849..73288387-chr2:73297041..73300553,5	K562	blood:

Variant related genes	Relation type
SFXN5	TF binding region
ENSG00000272702	Chromatin interaction
ENSG00000258881	Chromatin interaction
ENSG00000144040	Chromatin interaction
ENSG00000135624	Chromatin interaction
ENSG00000135617	Chromatin interaction
ENSG00000144043	Chromatin interaction
ENSG00000135631	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs17348624	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17348638	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17433172	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17504663	0.81[EUR][1000 genomes]
rs17504810	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17511570	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17570040	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17570432	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4143146	0.94[ASN][1000 genomes]
rs55633543	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55768189	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55801301	0.90[EUR][1000 genomes]
rs55854246	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55881165	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55938508	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56026282	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56161051	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56214999	0.93[ASN][1000 genomes]
rs56280862	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57522927	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57666506	0.84[EUR][1000 genomes]
rs57868938	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6706065	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73943009	0.90[EUR][1000 genomes]
rs73943014	0.92[EUR][1000 genomes]
rs73943015	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73943016	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73943017	0.88[EUR][1000 genomes]
rs73943034	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73943035	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73943036	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73943408	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73943410	0.85[ASN][1000 genomes]
rs73945731	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73945733	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73945734	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73945735	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73945740	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 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	chr2:73296200-73299600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr2:73296400-73297800	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr2:73296600-73297800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
4	chr2:73296600-73298000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr2:73296800-73298200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr2:73296800-73299000	Active TSS	Colonic Mucosa	Colon
7	chr2:73296800-73299000	Active TSS	Rectal Smooth Muscle	rectum
8	chr2:73296800-73299200	Active TSS	Left Ventricle	heart
9	chr2:73296800-73299200	Active TSS	HSMMtube	muscle
10	chr2:73297000-73297800	Flanking Active TSS	Fetal Stomach	stomach
11	chr2:73297000-73298000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr2:73297000-73299200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:73297000-73299200	Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr2:73297000-73299400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr2:73297000-73299400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:73297000-73299600	Active TSS	Fetal Kidney	kidney
17	chr2:73297200-73297800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr2:73297200-73297800	Active TSS	Brain Germinal Matrix	brain
19	chr2:73297200-73297800	Flanking Active TSS	Fetal Muscle Trunk	muscle
20	chr2:73297200-73299000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:73297200-73299200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr2:73297200-73299200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:73297200-73299200	Active TSS	A549	lung
24	chr2:73297200-73299200	Active TSS	GM12878-XiMat	blood
25	chr2:73297200-73299200	Active TSS	NHDF-Ad	bronchial
26	chr2:73297200-73299400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:73297200-73299400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:73297200-73299400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr2:73297200-73299400	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr2:73297200-73299400	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr2:73297200-73299400	Active TSS	Aorta	Aorta
32	chr2:73297200-73299400	Active TSS	Fetal Intestine Large	intestine
33	chr2:73297200-73299400	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr2:73297200-73299400	Bivalent/Poised TSS	HepG2	liver
35	chr2:73297200-73299600	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr2:73297200-73299800	Active TSS	Psoas Muscle	Psoas
37	chr2:73297400-73297800	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr2:73297400-73297800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:73297400-73297800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr2:73297400-73297800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:73297400-73298000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:73297400-73298000	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr2:73297400-73298200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:73297400-73298800	Active TSS	HMEC	breast
45	chr2:73297400-73299000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:73297400-73299000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:73297400-73299000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:73297400-73299000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:73297400-73299000	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr2:73297400-73299000	Active TSS	Primary hematopoietic stem cells short term culture	blood

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