Variant report

Variant	rs62278493
Chromosome Location	chr3:142442943-142442944
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:239)
CpG islands
(count:122)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:239 , 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	KAP1	chr3:142442937-142443166	HEK293	kidney:	n/a	n/a
2	POLR2A	chr3:142442806-142443197	GM12878	blood:	n/a	n/a
3	MAX	chr3:142442803-142443911	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr3:142442591-142444158	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:142442821-142443312	A549	lung:	n/a	n/a
6	POLR2A	chr3:142442540-142444139	K562	blood:	n/a	n/a
7	RCOR1	chr3:142442642-142444244	K562	blood:	n/a	n/a
8	GTF2F1	chr3:142442592-142443072	Hela-S3	cervix:	n/a	n/a
9	CEBPD	chr3:142442813-142443039	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:142442474-142444092	HCT-116	colon:	n/a	n/a
11	POLR2A	chr3:142442753-142443544	GM15510	blood:	n/a	n/a
12	E2F6	chr3:142442760-142443491	K562	blood:	n/a	chr3:142443361-142443370
13	STAT1	chr3:142442903-142442999	GM12878	blood:	n/a	n/a
14	CHD2	chr3:142442796-142443035	Hela-S3	cervix:	n/a	n/a
15	GTF2F1	chr3:142442874-142443076	K562	blood:	n/a	n/a
16	POLR2A	chr3:142442466-142444249	HepG2	liver:	n/a	n/a
17	ATF1	chr3:142442758-142443069	K562	blood:	n/a	n/a
18	MAX	chr3:142442654-142443332	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr3:142442780-142443089	GM12878	blood:	n/a	n/a
20	TAF1	chr3:142442490-142444141	H1-hESC	embryonic stem cell:	n/a	n/a
21	HDAC2	chr3:142442544-142443868	HepG2	liver:	n/a	chr3:142442657-142442666
22	CREB1	chr3:142442658-142443277	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAZ	chr3:142442566-142444005	K562	blood:	n/a	n/a
24	TBP	chr3:142442588-142443056	Hela-S3	cervix:	n/a	n/a
25	ZBTB7A	chr3:142442893-142443532	ECC-1	luminal epithelium:	n/a	chr3:142443356-142443364
26	POLR2A	chr3:142442842-142443285	PBDE	blood:	n/a	n/a
27	EGR1	chr3:142442657-142443015	K562	blood:	n/a	chr3:142442800-142442814
28	POLR2A	chr3:142442521-142444109	PFSK-1	brain:	n/a	n/a
29	MAX	chr3:142442803-142443188	K562	blood:	n/a	n/a
30	POLR2A	chr3:142442544-142444111	K562	blood:	n/a	n/a
31	TAF1	chr3:142442638-142443184	ECC-1	luminal epithelium:	n/a	n/a
32	TBP	chr3:142442629-142443156	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:142442581-142444190	HepG2	liver:	n/a	n/a
34	EP300	chr3:142442841-142443033	GM12878	blood:	n/a	n/a
35	RCOR1	chr3:142442739-142444123	HepG2	liver:	n/a	n/a
36	SMARCB1	chr3:142442645-142443942	Hela-S3	cervix:	n/a	n/a
37	CHD2	chr3:142442669-142443424	HepG2	liver:	n/a	n/a
38	ATF3	chr3:142442799-142442989	K562	blood:	n/a	n/a
39	EP300	chr3:142442939-142442986	HepG2	liver:	n/a	n/a
40	MXI1	chr3:142442921-142443084	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:142442824-142443582	HepG2	liver:	n/a	n/a
42	POLR2A	chr3:142442582-142443959	MCF-7	breast:	n/a	n/a
43	HMGN3	chr3:142442847-142443881	K562	blood:	n/a	n/a
44	CEBPB	chr3:142442939-142443087	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr3:142442566-142444053	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr3:142442789-142444213	K562	blood:	n/a	n/a
47	POLR2A	chr3:142442480-142444134	PANC-1	pancreas:	n/a	n/a
48	MYC	chr3:142442842-142443076	MCF-7	breast:	n/a	n/a
49	HEY1	chr3:142442424-142444236	HepG2	liver:	n/a	chr3:142443772-142443787 chr3:142443087-142443102
50	MAX	chr3:142442848-142444220	HepG2	liver:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142442934-142442984	AG10803	skin:	n/a
2	chr3:142442934-142442984	RPTEC	kidney:	n/a
3	chr3:142442934-142442984	AoSMC	blood vessel:	n/a
4	chr3:142442915-142442965	HMEC	breast:	n/a
5	chr3:142442934-142442984	HepG2	liver:	n/a
6	chr3:142442915-142442965	NT2-D1	testis:	n/a
7	chr3:142442934-142442984	GM12891	blood:	n/a
8	chr3:142442915-142442965	HCM	heart:	n/a
9	chr3:142442934-142442984	SAEC	small airway:	n/a
10	chr3:142442915-142442965	SK-N-SH_RA	brain:	n/a
11	chr3:142442934-142442984	NHDF-neo	bronchial:	n/a
12	chr3:142442934-142442984	HL-60	blood:	n/a
13	chr3:142442934-142442984	CMK	blood:	n/a
14	chr3:142442915-142442965	HepG2	liver:	n/a
15	chr3:142442915-142442965	BE2_C	brain:	n/a
16	chr3:142442915-142442965	NHBE	bronchial:	n/a
17	chr3:142442934-142442984	BE2_C	brain:	n/a
18	chr3:142442934-142442984	NB4	blood:	n/a
19	chr3:142442915-142442965	SAEC	small airway:	n/a
20	chr3:142442915-142442965	AG04450	lung:	fetal
21	chr3:142442934-142442984	PANC-1	pancreas:	n/a
22	chr3:142442934-142442984	NH-A	brain:	n/a
23	chr3:142442934-142442984	HCT-116	colon:	n/a
24	chr3:142442915-142442965	Hela-S3	cervix:	n/a
25	chr3:142442934-142442984	AG09319	gingival:	n/a
26	chr3:142442915-142442965	AG09309	skin:	n/a
27	chr3:142442934-142442984	PFSK-1	brain:	n/a
28	chr3:142442915-142442965	AG10803	skin:	n/a
29	chr3:142442934-142442984	LNCaP	prostate:	n/a
30	chr3:142442934-142442984	SK-N-SH_RA	brain:	n/a
31	chr3:142442934-142442984	GM19239	blood:	n/a
32	chr3:142442934-142442984	HRE	kidney:	n/a
33	chr3:142442915-142442965	HCT-116	colon:	n/a
34	chr3:142442915-142442965	NH-A	brain:	n/a
35	chr3:142442934-142442984	ovcar-3	ovarian:	n/a
36	chr3:142442934-142442984	HEK293	kidney:	embryo
37	chr3:142442934-142442984	NT2-D1	testis:	n/a
38	chr3:142442915-142442965	HRCEpiC	kidney:	n/a
39	chr3:142442915-142442965	GM06990	blood:	n/a
40	chr3:142442934-142442984	K562	blood:	n/a
41	chr3:142442915-142442965	HCF	heart:	n/a
42	chr3:142442934-142442984	NHBE	bronchial:	n/a
43	chr3:142442915-142442965	HPAEpiC	pulmonary alveolar:	n/a
44	chr3:142442915-142442965	AG09319	gingival:	n/a
45	chr3:142442915-142442965	ECC-1	luminal epithelium:	n/a
46	chr3:142442915-142442965	HRPEpiC	eye:	n/a
47	chr3:142442934-142442984	HNPCEpiC	eye:	n/a
48	chr3:142442934-142442984	H1-hESC	embryonic stem cell:	embryo
49	chr3:142442934-142442984	Hela-S3	cervix:	n/a
50	chr3:142442934-142442984	AG09309	skin:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142442669..142444351-chr3:142720029..142722522,2	MCF-7	breast:
2	chr3:142312229..142317018-chr3:142442889..142445391,9	K562	blood:
3	chr3:142442891..142443401-chr9:140082899..140083506,2	Hela-S3	cervix:
4	chr3:142442417..142444804-chr3:142718685..142721847,4	K562	blood:
5	chr11:71823293..71823861-chr3:142442823..142443406,2	NB4	blood:
6	chr3:142313378..142316741-chr3:142442748..142446550,8	K562	blood:
7	chr3:142295996..142297624-chr3:142440935..142443594,2	K562	blood:
8	chr3:142297625..142299268-chr3:142441632..142444151,3	K562	blood:
9	chr3:142314524..142316871-chr3:142442608..142445149,2	MCF-7	breast:
10	chr3:142297625..142299268-chr3:142441632..142445353,4	K562	blood:

No data

Variant related genes	Relation type
TRPC1	TF binding region
TRPC1	CpG island
ENSG00000175054	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000176248	Chromatin interaction
ENSG00000110200	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000176101	Chromatin interaction
ENSG00000268129	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10935467	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11915810	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11929069	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13060062	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13064897	0.85[AMR][1000 genomes]
rs13081255	0.85[AMR][1000 genomes]
rs13087943	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13092601	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13094259	0.85[EUR][1000 genomes]
rs1916638	0.84[AMR][1000 genomes]
rs34084493	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34485065	0.88[AMR][1000 genomes]
rs34941168	0.86[EUR][1000 genomes]
rs36085850	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55968753	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62278490	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278492	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278494	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62278495	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142442000-142443400	Active TSS	Brain Germinal Matrix	brain
2	chr3:142442200-142443400	Active TSS	Fetal Brain Female	brain
3	chr3:142442200-142443800	Active TSS	Brain Anterior Caudate	brain
4	chr3:142442200-142444200	Active TSS	Aorta	Aorta
5	chr3:142442200-142444200	Active TSS	Brain Angular Gyrus	brain
6	chr3:142442200-142444200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:142442200-142444400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:142442200-142444600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:142442200-142444600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr3:142442200-142444600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:142442200-142444800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:142442200-142444800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:142442200-142444800	Active TSS	K562	blood
14	chr3:142442200-142445000	Active TSS	A549	lung
15	chr3:142442400-142443000	Active TSS	Primary hematopoietic stem cells	blood
16	chr3:142442400-142443000	Active TSS	Colonic Mucosa	Colon
17	chr3:142442400-142443200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:142442400-142443200	Active TSS	Fetal Intestine Large	intestine
19	chr3:142442400-142443400	Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr3:142442400-142443400	Bivalent/Poised TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:142442400-142443400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:142442400-142443400	Active TSS	Duodenum Mucosa	Duodenum
23	chr3:142442400-142443400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr3:142442400-142443400	Active TSS	Fetal Muscle Trunk	muscle
25	chr3:142442400-142443400	Active TSS	Fetal Stomach	stomach
26	chr3:142442400-142443400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr3:142442400-142443400	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr3:142442400-142443400	Active TSS	GM12878-XiMat	blood
29	chr3:142442400-142443600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:142442400-142443600	Active TSS	Fetal Muscle Leg	muscle
31	chr3:142442400-142443800	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr3:142442400-142443800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:142442400-142443800	Active TSS	Hela-S3	cervix
34	chr3:142442400-142443800	Active TSS	HUVEC	blood vessel
35	chr3:142442400-142443800	Active TSS	NH-A	brain
36	chr3:142442400-142443800	Active TSS	NHEK	skin
37	chr3:142442400-142444000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:142442400-142444000	Active TSS	Brain Cingulate Gyrus	brain
39	chr3:142442400-142444000	Active TSS	Brain Hippocampus Middle	brain
40	chr3:142442400-142444000	Active TSS	Brain Substantia Nigra	brain
41	chr3:142442400-142444000	Active TSS	Fetal Lung	lung
42	chr3:142442400-142444000	Active TSS	HMEC	breast
43	chr3:142442400-142444200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:142442400-142444200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:142442400-142444200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:142442400-142444200	Active TSS	Muscle Satellite Cultured Cells	--
47	chr3:142442400-142444200	Active TSS	Right Ventricle	heart
48	chr3:142442400-142444200	Active TSS	HSMMtube	muscle
49	chr3:142442400-142444400	Active TSS	H9 Cell Line	embryonic stem cell
50	chr3:142442400-142444400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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