Variant report

Variant	rs62278492
Chromosome Location	chr3:142442660-142442661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:107)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:107 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:142442591-142444158	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:142442540-142444139	K562	blood:	n/a	n/a
3	RCOR1	chr3:142442642-142444244	K562	blood:	n/a	n/a
4	GTF2F1	chr3:142442592-142443072	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:142442474-142444092	HCT-116	colon:	n/a	n/a
6	POLR2A	chr3:142442466-142444249	HepG2	liver:	n/a	n/a
7	MAX	chr3:142442654-142443332	ECC-1	luminal epithelium:	n/a	n/a
8	TAF1	chr3:142442490-142444141	H1-hESC	embryonic stem cell:	n/a	n/a
9	HEY1	chr3:142442570-142442796	HepG2	liver:	n/a	n/a
10	HDAC2	chr3:142442544-142443868	HepG2	liver:	n/a	chr3:142442657-142442666
11	CREB1	chr3:142442658-142443277	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAZ	chr3:142442566-142444005	K562	blood:	n/a	n/a
13	TBP	chr3:142442588-142443056	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:142442637-142442789	H1-hESC	embryonic stem cell:	n/a	n/a
15	EGR1	chr3:142442657-142443015	K562	blood:	n/a	chr3:142442800-142442814
16	POLR2A	chr3:142442521-142444109	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr3:142442544-142444111	K562	blood:	n/a	n/a
18	TAF1	chr3:142442638-142443184	ECC-1	luminal epithelium:	n/a	n/a
19	TBP	chr3:142442629-142443156	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:142442581-142444190	HepG2	liver:	n/a	n/a
21	SMARCB1	chr3:142442645-142443942	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:142442582-142443959	MCF-7	breast:	n/a	n/a
23	POLR2A	chr3:142442557-142442794	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr3:142442566-142444053	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr3:142442480-142444134	PANC-1	pancreas:	n/a	n/a
26	RUNX3	chr3:142442486-142442919	GM12878	blood:	n/a	n/a
27	HEY1	chr3:142442424-142444236	HepG2	liver:	n/a	chr3:142443772-142443787 chr3:142443087-142443102
28	POLR2A	chr3:142442493-142443051	SK-N-SH	brain:	n/a	n/a
29	SIN3AK20	chr3:142442655-142443105	HCT-116	colon:	n/a	n/a
30	POLR2A	chr3:142442541-142443931	U87	brain:	n/a	n/a
31	POLR2A	chr3:142442571-142444003	PANC-1	pancreas:	n/a	n/a
32	EGR1	chr3:142442627-142442994	K562	blood:	n/a	chr3:142442800-142442814
33	RAD21	chr3:142442521-142443040	SK-N-SH_RA	brain:	n/a	chr3:142442757-142442770
34	POLR2A	chr3:142442615-142442821	HepG2	liver:	n/a	n/a
35	TAF1	chr3:142442615-142444006	HepG2	liver:	n/a	n/a
36	RCOR1	chr3:142442605-142443043	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:142442572-142444229	U87	brain:	n/a	n/a
38	POLR2A	chr3:142442600-142443858	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr3:142442530-142443856	Raji	blood:	n/a	n/a
40	IRF1	chr3:142442560-142443088	K562	blood:	n/a	n/a
41	POLR2A	chr3:142442478-142443141	ECC-1	luminal epithelium:	n/a	n/a
42	JUN	chr3:142442470-142443168	K562	blood:	n/a	n/a
43	POLR2A	chr3:142442560-142444015	K562	blood:	n/a	n/a
44	POLR2A	chr3:142442576-142443359	NB4	blood:	n/a	n/a
45	POLR2A	chr3:142442486-142444406	H1-hESC	embryonic stem cell:	n/a	n/a
46	TBP	chr3:142442561-142444117	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:142442541-142443990	HCT-116	colon:	n/a	n/a
48	TBP	chr3:142442621-142444116	K562	blood:	n/a	n/a
49	POLR2A	chr3:142442549-142444171	HEK293	kidney:	n/a	n/a
50	NFIC	chr3:142442574-142443163	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142442417..142444804-chr3:142718685..142721847,4	K562	blood:
2	chr3:142295996..142297624-chr3:142440935..142443594,2	K562	blood:
3	chr3:142297625..142299268-chr3:142441632..142444151,3	K562	blood:
4	chr3:142314524..142316871-chr3:142442608..142445149,2	MCF-7	breast:
5	chr3:142297625..142299268-chr3:142441632..142445353,4	K562	blood:

No data

Variant related genes	Relation type
TRPC1	TF binding region
ENSG00000163714	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000175054	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	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11915810	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11929069	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13060062	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13064897	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13081255	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13087943	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13092601	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13094259	0.85[EUR][1000 genomes]
rs1916638	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34084493	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs34485065	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs34941168	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36085850	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs55968753	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62278490	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278493	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278494	0.89[AFR][1000 genomes];0.88[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:115 , 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	chr3:142442200-142442800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:142442200-142442800	Flanking Active TSS	Dnd41	blood
4	chr3:142442200-142443400	Active TSS	Fetal Brain Female	brain
5	chr3:142442200-142443800	Active TSS	Brain Anterior Caudate	brain
6	chr3:142442200-142444200	Active TSS	Aorta	Aorta
7	chr3:142442200-142444200	Active TSS	Brain Angular Gyrus	brain
8	chr3:142442200-142444200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:142442200-142444400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:142442200-142444600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:142442200-142444600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr3:142442200-142444600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:142442200-142444800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:142442200-142444800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr3:142442200-142444800	Active TSS	K562	blood
16	chr3:142442200-142445000	Active TSS	A549	lung
17	chr3:142442400-142442800	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr3:142442400-142442800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr3:142442400-142442800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr3:142442400-142442800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:142442400-142442800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:142442400-142442800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:142442400-142442800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr3:142442400-142442800	Flanking Active TSS	Fetal Thymus	thymus
25	chr3:142442400-142442800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr3:142442400-142443000	Active TSS	Primary hematopoietic stem cells	blood
27	chr3:142442400-142443000	Active TSS	Colonic Mucosa	Colon
28	chr3:142442400-142443200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:142442400-142443200	Active TSS	Fetal Intestine Large	intestine
30	chr3:142442400-142443400	Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr3:142442400-142443400	Bivalent/Poised TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:142442400-142443400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:142442400-142443400	Active TSS	Duodenum Mucosa	Duodenum
34	chr3:142442400-142443400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr3:142442400-142443400	Active TSS	Fetal Muscle Trunk	muscle
36	chr3:142442400-142443400	Active TSS	Fetal Stomach	stomach
37	chr3:142442400-142443400	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr3:142442400-142443400	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr3:142442400-142443400	Active TSS	GM12878-XiMat	blood
40	chr3:142442400-142443600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:142442400-142443600	Active TSS	Fetal Muscle Leg	muscle
42	chr3:142442400-142443800	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr3:142442400-142443800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:142442400-142443800	Active TSS	Hela-S3	cervix
45	chr3:142442400-142443800	Active TSS	HUVEC	blood vessel
46	chr3:142442400-142443800	Active TSS	NH-A	brain
47	chr3:142442400-142443800	Active TSS	NHEK	skin
48	chr3:142442400-142444000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:142442400-142444000	Active TSS	Brain Cingulate Gyrus	brain
50	chr3:142442400-142444000	Active TSS	Brain Hippocampus Middle	brain

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