Variant report

Variant	rs4146774
Chromosome Location	chr3:112738644-112738645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:391)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:391 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:112737462-112738876	GM18505	blood:	n/a	n/a
2	POLR2A	chr3:112737749-112739026	U87	brain:	n/a	n/a
3	ZBTB7A	chr3:112737886-112738714	ECC-1	luminal epithelium:	n/a	chr3:112738267-112738274
4	TAF1	chr3:112737993-112738753	GM12878	blood:	n/a	n/a
5	MYC	chr3:112738150-112738847	H1-hESC	embryonic stem cell:	n/a	chr3:112738310-112738320
6	RCOR1	chr3:112738274-112739024	K562	blood:	n/a	n/a
7	E2F4	chr3:112738336-112738765	MCF10A-Er-Src	breast:	n/a	chr3:112738607-112738617
8	TEAD4	chr3:112738273-112738749	K562	blood:	n/a	n/a
9	GABPA	chr3:112737831-112738916	MCF-7	breast:	n/a	chr3:112738311-112738320 chr3:112738262-112738271
10	USF1	chr3:112738572-112738799	HepG2	liver:	n/a	chr3:112738693-112738704 chr3:112738606-112738622
11	USF2	chr3:112738626-112738826	HepG2	liver:	n/a	chr3:112738693-112738704
12	MYC	chr3:112738409-112738791	HUVEC	blood vessel:	n/a	n/a
13	CREB1	chr3:112738095-112738817	A549	lung:	n/a	n/a
14	ELF1	chr3:112738191-112738685	A549	lung:	n/a	n/a
15	POLR2A	chr3:112737668-112738999	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr3:112737347-112738913	GM12878	blood:	n/a	n/a
17	MXI1	chr3:112738078-112738851	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr3:112737888-112739033	MCF-7	breast:	n/a	chr3:112738310-112738320
19	POLR2A	chr3:112737210-112739083	SK-N-MC	brain:	n/a	n/a
20	MAX	chr3:112737842-112739103	HepG2	liver:	n/a	chr3:112738310-112738320
21	POLR2A	chr3:112737976-112738759	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:112736649-112739006	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:112737122-112738647	GM12878	blood:	n/a	n/a
24	TAF1	chr3:112737943-112738668	H1-hESC	embryonic stem cell:	n/a	n/a
25	RUNX3	chr3:112738005-112739166	GM12878	blood:	n/a	n/a
26	ELF1	chr3:112738202-112738739	A549	lung:	n/a	n/a
27	POLR2A	chr3:112737931-112738816	A549	lung:	n/a	n/a
28	POLR2A	chr3:112737507-112738795	GM12878	blood:	n/a	n/a
29	MXI1	chr3:112736597-112739325	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr3:112737944-112738823	MCF-7	breast:	n/a	n/a
31	MYC	chr3:112738007-112738802	MCF-7	breast:	n/a	chr3:112738310-112738320
32	POLR2A	chr3:112737951-112738842	HepG2	liver:	n/a	n/a
33	MYC	chr3:112738524-112738842	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:112737979-112738885	GM15510	blood:	n/a	n/a
35	POLR2A	chr3:112737644-112738856	Hela-S3	cervix:	n/a	n/a
36	GABPA	chr3:112738181-112738664	GM12878	blood:	n/a	chr3:112738311-112738320 chr3:112738262-112738271
37	YY1	chr3:112737912-112738824	GM12891	blood:	n/a	n/a
38	GABPA	chr3:112737885-112738732	Hela-S3	cervix:	n/a	chr3:112738311-112738320 chr3:112738262-112738271
39	YY1	chr3:112737889-112738836	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:112737440-112738867	Hela-S3	cervix:	n/a	n/a
41	USF1	chr3:112738489-112738783	A549	lung:	n/a	chr3:112738693-112738704 chr3:112738606-112738622
42	YY1	chr3:112737940-112738866	GM12878	blood:	n/a	n/a
43	STAT3	chr3:112737989-112738679	MCF10A-Er-Src	breast:	n/a	chr3:112738362-112738374
44	POLR2A	chr3:112737366-112738731	GM12891	blood:	n/a	n/a
45	MYC	chr3:112737773-112739493	A549	lung:	n/a	chr3:112738310-112738320
46	FOS	chr3:112738541-112738836	MCF10A-Er-Src	breast:	n/a	n/a
47	GABPA	chr3:112737790-112738962	MCF-7	breast:	n/a	chr3:112738311-112738320 chr3:112738262-112738271
48	E2F6	chr3:112738118-112738980	H1-hESC	embryonic stem cell:	n/a	chr3:112738607-112738617
49	MYC	chr3:112737716-112739051	K562	blood:	n/a	chr3:112738310-112738320
50	MYC	chr3:112738276-112738883	K562	blood:	n/a	chr3:112738310-112738320

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:112738642-112738692	AG09319	gingival:	n/a
2	chr3:112738642-112738692	AG10803	skin:	n/a
3	chr3:112738642-112738692	AG09309	skin:	n/a
4	chr3:112738642-112738692	HRE	kidney:	n/a
5	chr3:112738642-112738692	Hela-S3	cervix:	n/a
6	chr3:112738642-112738692	Caco-2	colon:	n/a
7	chr3:112738642-112738692	SKMC	muscle:	n/a
8	chr3:112738642-112738692	AoSMC	blood vessel:	n/a
9	chr3:112738642-112738692	GM19239	blood:	n/a
10	chr3:112738642-112738692	SK-N-SH_RA	brain:	n/a
11	chr3:112738642-112738692	BJ	skin:	n/a
12	chr3:112738642-112738692	SK-N-MC	brain:	n/a
13	chr3:112738642-112738692	U87	brain:	n/a
14	chr3:112738642-112738692	GM12878	blood:	n/a
15	chr3:112738642-112738692	K562	blood:	n/a
16	chr3:112738642-112738692	A549	lung:	n/a
17	chr3:112738642-112738692	HRCEpiC	kidney:	n/a
18	chr3:112738642-112738692	HCM	heart:	n/a
19	chr3:112738642-112738692	SAEC	small airway:	n/a
20	chr3:112738642-112738692	HL-60	blood:	n/a
21	chr3:112738642-112738692	CMK	blood:	n/a
22	chr3:112738642-112738692	GM06990	blood:	n/a
23	chr3:112738642-112738692	ECC-1	luminal epithelium:	n/a
24	chr3:112738642-112738692	NHBE	bronchial:	n/a
25	chr3:112738642-112738692	HCT-116	colon:	n/a
26	chr3:112738642-112738692	ProgFib	skin:	n/a
27	chr3:112738642-112738692	AG04450	lung:	fetal
28	chr3:112738642-112738692	HCF	heart:	n/a
29	chr3:112738642-112738692	T-47D	breast:	n/a
30	chr3:112738642-112738692	HNPCEpiC	eye:	n/a
31	chr3:112738642-112738692	HIPEpiC	eye:	n/a
32	chr3:112738642-112738692	HEEpiC	esophagus:	n/a
33	chr3:112738642-112738692	IMR90	lung:	fetal
34	chr3:112738642-112738692	BE2_C	brain:	n/a
35	chr3:112738642-112738692	SK-N-SH	brain:	n/a
36	chr3:112738642-112738692	HUVEC	blood vessel:	n/a
37	chr3:112738642-112738692	MCF-7	breast:	n/a
38	chr3:112738642-112738692	GM12891	blood:	n/a
39	chr3:112738642-112738692	MCF10A-Er-Src	breast:	n/a
40	chr3:112738642-112738692	GM12892	blood:	n/a
41	chr3:112738642-112738692	PANC-1	pancreas:	n/a
42	chr3:112738642-112738692	NB4	blood:	n/a
43	chr3:112738642-112738692	NHDF-neo	bronchial:	n/a
44	chr3:112738642-112738692	ovcar-3	ovarian:	n/a
45	chr3:112738642-112738692	RPTEC	kidney:	n/a
46	chr3:112738642-112738692	Hepatocyte	liver:	n/a
47	chr3:112738642-112738692	PFSK-1	brain:	n/a
48	chr3:112738642-112738692	Jurkat	blood:	n/a
49	chr3:112738642-112738692	NH-A	brain:	n/a
50	chr3:112738642-112738692	HCPEpiC	choroid plexus:	n/a

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:112709241..112710011-chr3:112737824..112738662,2	HCT-116	colon:
2	chr3:112726403..112732813-chr3:112735056..112739637,9	MCF-7	breast:
3	chr3:112709706..112712038-chr3:112736780..112739124,2	MCF-7	breast:
4	chr3:112738070..112738697-chr5:75013074..75013717,2	HCT-116	colon:
5	chr3:112358855..112360949-chr3:112737036..112738900,2	K562	blood:
6	chr3:112358697..112360499-chr3:112735766..112739410,3	MCF-7	breast:
7	chr3:112727442..112729984-chr3:112737783..112739677,2	MCF-7	breast:
8	chr3:112730174..112733803-chr3:112737181..112739606,5	MCF-7	breast:
9	chr3:112358680..112360592-chr3:112737016..112739347,2	MCF-7	breast:
10	chr3:112737944..112740909-chr3:112760087..112762982,2	MCF-7	breast:
11	chr3:112279739..112282135-chr3:112735331..112738696,3	K562	blood:
12	chr3:112708547..112711309-chr3:112736671..112738787,3	MCF-7	breast:
13	chr3:112708559..112710573-chr3:112736590..112739999,3	K562	blood:

No data

Variant related genes	Relation type
C3orf17	TF binding region
C3orf17	CpG island
ENSG00000144848	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000152359	Chromatin interaction
ENSG00000243483	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10934208	1.00[AFR][1000 genomes]
rs10934209	1.00[AFR][1000 genomes]
rs2293559	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56666099	1.00[AFR][1000 genomes]
rs56820451	1.00[AFR][1000 genomes]
rs57287136	1.00[AFR][1000 genomes]
rs57360909	1.00[AFR][1000 genomes]
rs58105957	1.00[AFR][1000 genomes]
rs60481719	1.00[AFR][1000 genomes]
rs60671920	1.00[AFR][1000 genomes]
rs61191442	1.00[AFR][1000 genomes]
rs61526975	1.00[AFR][1000 genomes]
rs61674636	1.00[AFR][1000 genomes]
rs6781014	0.86[ASN][1000 genomes]
rs72491118	1.00[AFR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112736200-112738800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:112736600-112739000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:112736800-112738800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:112737000-112738800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:112737000-112738800	Active TSS	GM12878-XiMat	blood
6	chr3:112737000-112738800	Active TSS	HSMMtube	muscle
7	chr3:112737000-112739000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr3:112737000-112739000	Active TSS	Psoas Muscle	Psoas
9	chr3:112737000-112739000	Active TSS	Right Ventricle	heart
10	chr3:112737000-112739200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:112737000-112739200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:112737000-112739200	Active TSS	Fetal Muscle Trunk	muscle
13	chr3:112737200-112738800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr3:112737200-112738800	Active TSS	H1 Cell Line	embryonic stem cell
15	chr3:112737200-112738800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:112737200-112738800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:112737200-112738800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:112737200-112738800	Active TSS	NHDF-Ad	bronchial
19	chr3:112737200-112739000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:112737200-112739000	Active TSS	Aorta	Aorta
21	chr3:112737200-112739000	Active TSS	Colonic Mucosa	Colon
22	chr3:112737200-112739200	Active TSS	Right Atrium	heart
23	chr3:112737200-112739200	Active TSS	A549	lung
24	chr3:112737200-112739200	Active TSS	HSMM	muscle
25	chr3:112737400-112738800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr3:112737400-112738800	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr3:112737400-112738800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:112737400-112738800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:112737400-112738800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:112737400-112738800	Active TSS	Muscle Satellite Cultured Cells	--
31	chr3:112737400-112738800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:112737400-112738800	Active TSS	Fetal Intestine Large	intestine
33	chr3:112737400-112738800	Active TSS	Fetal Kidney	kidney
34	chr3:112737400-112738800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr3:112737400-112738800	Active TSS	Fetal Stomach	stomach
36	chr3:112737400-112738800	Active TSS	Pancreas	Pancrea
37	chr3:112737400-112738800	Active TSS	NHLF	lung
38	chr3:112737400-112739000	Active TSS	Fetal Brain Female	brain
39	chr3:112737400-112739000	Active TSS	Left Ventricle	heart
40	chr3:112737400-112739000	Active TSS	Lung	lung
41	chr3:112737400-112739000	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr3:112737400-112739200	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr3:112737400-112739200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:112737400-112739200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:112737400-112739200	Active TSS	Fetal Brain Male	brain
46	chr3:112737600-112738800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr3:112737600-112738800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:112737600-112738800	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr3:112737600-112738800	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr3:112737600-112738800	Active TSS	Brain Cingulate Gyrus	brain

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