Variant report

Variant	rs12025460
Chromosome Location	chr1:220921502-220921503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:218)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:218 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:220921285-220921874	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:220921342-220921963	GM12892	blood:	n/a	n/a
3	ELF1	chr1:220921332-220921950	MCF-7	breast:	n/a	n/a
4	POLR2A	chr1:220921488-220921783	SK-N-SH	brain:	n/a	n/a
5	BHLHE40	chr1:220921271-220921720	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:220921372-220922192	MCF-7	breast:	n/a	n/a
7	REST	chr1:220921352-220921751	A549	lung:	n/a	n/a
8	POLR2A	chr1:220921280-220922190	A549	lung:	n/a	n/a
9	RAD21	chr1:220921269-220921518	Hela-S3	cervix:	n/a	n/a
10	TAF1	chr1:220921327-220921794	SK-N-SH	brain:	n/a	n/a
11	USF1	chr1:220921354-220921774	A549	lung:	n/a	n/a
12	CEBPB	chr1:220921063-220921727	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr1:220921400-220921550	AG10803	skin:	n/a	n/a
14	POLR2A	chr1:220921387-220921891	MCF10A-Er-Src	breast:	n/a	n/a
15	ELK1	chr1:220921320-220921757	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:220921314-220921965	A549	lung:	n/a	n/a
17	MYC	chr1:220921074-220922070	NB4	blood:	n/a	n/a
18	PML	chr1:220921423-220921919	MCF-7	breast:	n/a	n/a
19	TCF7L2	chr1:220921284-220922187	HCT-116	colon:	n/a	n/a
20	TAF1	chr1:220921411-220922199	HepG2	liver:	n/a	n/a
21	CEBPB	chr1:220921254-220921647	HepG2	liver:	n/a	n/a
22	CREB1	chr1:220921184-220922070	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:220921340-220921926	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:220921204-220922300	Hela-S3	cervix:	n/a	n/a
25	CTBP2	chr1:220921308-220922346	H1-hESC	embryonic stem cell:	n/a	n/a
26	TCF12	chr1:220921372-220922070	ECC-1	luminal epithelium:	n/a	n/a
27	MAX	chr1:220921059-220922326	H1-hESC	embryonic stem cell:	n/a	chr1:220922195-220922205
28	POLR2A	chr1:220921284-220922227	MCF-7	breast:	n/a	n/a
29	YY1	chr1:220921327-220922277	HepG2	liver:	n/a	chr1:220922166-220922177
30	MAX	chr1:220921268-220922014	SK-N-SH	brain:	n/a	n/a
31	FOXA2	chr1:220921237-220921660	HepG2	liver:	n/a	n/a
32	CTCF	chr1:220921420-220921570	HPAF	blood vessel:	n/a	n/a
33	POLR2A	chr1:220921131-220922327	Hela-S3	cervix:	n/a	n/a
34	CHD2	chr1:220921300-220921846	HepG2	liver:	n/a	n/a
35	YY1	chr1:220921409-220921796	GM12892	blood:	n/a	n/a
36	POLR2A	chr1:220921247-220921866	PANC-1	pancreas:	n/a	n/a
37	MAZ	chr1:220921336-220921762	HepG2	liver:	n/a	n/a
38	CEBPB	chr1:220921254-220921591	IMR90	lung:	n/a	n/a
39	ETS1	chr1:220921268-220921721	A549	lung:	n/a	n/a
40	TBP	chr1:220921073-220921854	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr1:220921360-220921510	BJ	skin:	n/a	n/a
42	YY1	chr1:220921285-220921903	SK-N-SH_RA	brain:	n/a	n/a
43	SMARCB1	chr1:220921175-220922275	Hela-S3	cervix:	n/a	n/a
44	YY1	chr1:220921375-220921995	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr1:220921269-220922281	GM12892	blood:	n/a	n/a
46	POLR2A	chr1:220921425-220922094	GM18505	blood:	n/a	n/a
47	E2F6	chr1:220920973-220922388	H1-hESC	embryonic stem cell:	n/a	chr1:220922158-220922167
48	POLR2A	chr1:220921280-220921969	HUVEC	blood vessel:	n/a	n/a
49	TBP	chr1:220921240-220921844	HepG2	liver:	n/a	n/a
50	TAF1	chr1:220921249-220922078	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:220862132..220866220-chr1:220920879..220923309,4	MCF-7	breast:
2	chr1:220920704..220923005-chr1:220929506..220932087,2	MCF-7	breast:
3	chr1:202857727..202858610-chr1:220921308..220922105,2	Hela-S3	cervix:
4	chr1:220920532..220923272-chr1:220926936..220929369,4	MCF-7	breast:
5	chr1:220920087..220922800-chr1:220958239..220960991,2	MCF-7	breast:
6	chr1:220921252..220921799-chr7:128695148..128695707,2	NB4	blood:

No data

Variant related genes	Relation type
MARC2	TF binding region
ENSG00000186205	Chromatin interaction
ENSG00000117791	Chromatin interaction
ENSG00000183155	Chromatin interaction
ENSG00000162817	Chromatin interaction
ENSG00000064419	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12023149	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12027298	0.82[ASN][1000 genomes]
rs12027302	0.82[ASN][1000 genomes]
rs12027337	0.82[ASN][1000 genomes]
rs12034895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12038621	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12042585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12043602	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044903	0.82[ASN][1000 genomes]
rs12045050	0.82[ASN][1000 genomes]
rs12045953	1.00[EUR][1000 genomes]
rs12048193	0.82[ASN][1000 genomes]
rs17008338	0.91[ASN][1000 genomes]
rs35297838	0.94[ASN][1000 genomes]
rs58538649	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60087444	1.00[EUR][1000 genomes]
rs60183673	0.80[ASN][1000 genomes]
rs72472309	1.00[EUR][1000 genomes]
rs72472366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72472379	0.82[ASN][1000 genomes]
rs72472380	0.82[ASN][1000 genomes]
rs72472383	0.82[ASN][1000 genomes]
rs72472384	0.82[ASN][1000 genomes]
rs7545562	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv160470	chr1:220919015-220922779	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220920600-220921600	Flanking Active TSS	Fetal Muscle Leg	muscle
2	chr1:220920600-220922600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:220920600-220922800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:220920800-220921600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
5	chr1:220920800-220921600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:220920800-220921600	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr1:220920800-220922400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:220920800-220922400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:220920800-220922600	Active TSS	Left Ventricle	heart
10	chr1:220920800-220922800	Active TSS	Fetal Kidney	kidney
11	chr1:220920800-220924000	Active TSS	Brain Anterior Caudate	brain
12	chr1:220920800-220924000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr1:220920800-220924200	Active TSS	Brain Angular Gyrus	brain
14	chr1:220921000-220921600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:220921000-220921600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:220921000-220921600	Flanking Active TSS	HUVEC	blood vessel
17	chr1:220921000-220921600	Flanking Active TSS	NH-A	brain
18	chr1:220921000-220921600	Flanking Active TSS	Osteobl	bone
19	chr1:220921000-220922000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr1:220921000-220922400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:220921000-220922400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:220921000-220922400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:220921000-220922600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:220921000-220922600	Active TSS	Psoas Muscle	Psoas
25	chr1:220921000-220922800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:220921000-220922800	Active TSS	Ovary	ovary
27	chr1:220921000-220922800	Active TSS	Right Ventricle	heart
28	chr1:220921000-220923600	Active TSS	Right Atrium	heart
29	chr1:220921200-220921600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:220921200-220921600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
31	chr1:220921200-220921600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
32	chr1:220921200-220921600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
33	chr1:220921200-220921600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:220921200-220921600	Flanking Active TSS	Placenta	Placenta
35	chr1:220921200-220921600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
36	chr1:220921200-220921600	Flanking Active TSS	HSMM	muscle
37	chr1:220921200-220921600	Flanking Active TSS	HSMMtube	muscle
38	chr1:220921200-220921800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
39	chr1:220921200-220921800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:220921200-220921800	Bivalent/Poised TSS	NHEK	skin
41	chr1:220921200-220922000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:220921200-220922200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:220921200-220922200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:220921200-220922400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:220921200-220922400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:220921200-220922400	Active TSS	Brain Substantia Nigra	brain
47	chr1:220921200-220922400	Active TSS	Colonic Mucosa	Colon
48	chr1:220921200-220922400	Active TSS	Lung	lung
49	chr1:220921200-220922400	Active TSS	Placenta Amnion	Placenta Amnion
50	chr1:220921200-220922400	Active TSS	A549	lung

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