Variant report

Variant	rs62246379
Chromosome Location	chr3:47021837-47021838
allele	A/G
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	MXI1	chr3:47020475-47021913	IMR90	lung:	n/a	n/a
2	MAX	chr3:47020395-47021897	A549	lung:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
3	HA-E2F1	chr3:47020589-47021847	MCF-7	breast:	n/a	chr3:47020871-47020880 chr3:47020710-47020722 chr3:47020890-47020901 chr3:47021293-47021302 chr3:47021236-47021245
4	HCFC1	chr3:47020564-47021913	Hela-S3	cervix:	n/a	n/a
5	CTBP2	chr3:47020488-47021916	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAZ	chr3:47020868-47021995	GM12878	blood:	n/a	n/a
7	YY1	chr3:47020571-47021859	HepG2	liver:	n/a	chr3:47020665-47020676 chr3:47021013-47021024 chr3:47020871-47020880 chr3:47021143-47021152 chr3:47021109-47021123 chr3:47021107-47021118 chr3:47021293-47021302
8	MXI1	chr3:47020382-47022110	SK-N-SH	brain:	n/a	n/a
9	MAX	chr3:47020321-47021924	K562	blood:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
10	POLR2A	chr3:47020633-47021912	HUVEC	blood vessel:	n/a	n/a
11	SIN3A	chr3:47020624-47021920	H1-hESC	embryonic stem cell:	n/a	chr3:47021236-47021247
12	POLR2A	chr3:47020331-47021965	Raji	blood:	n/a	n/a
13	POLR2A	chr3:47021713-47022639	MCF-7	breast:	n/a	n/a
14	MYC	chr3:47020777-47021850	A549	lung:	n/a	n/a
15	MAX	chr3:47020556-47021840	ECC-1	luminal epithelium:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
16	POLR2A	chr3:47020562-47021866	HL-60	blood:	n/a	n/a
17	GTF3C2	chr3:47020569-47021945	K562	blood:	n/a	n/a
18	POLR2A	chr3:47021765-47021946	MCF-7	breast:	n/a	n/a
19	MAX	chr3:47020425-47021846	HepG2	liver:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
20	ZBTB7A	chr3:47021699-47022086	K562	blood:	n/a	chr3:47021835-47021846 chr3:47021834-47021845
21	MAX	chr3:47020872-47021904	NB4	blood:	n/a	n/a
22	POLR2A	chr3:47020469-47022022	K562	blood:	n/a	n/a
23	ELF1	chr3:47020462-47021871	GM12878	blood:	n/a	chr3:47021334-47021346 chr3:47021698-47021710
24	MYC	chr3:47020716-47021953	NB4	blood:	n/a	n/a
25	CHD2	chr3:47021782-47021935	Hela-S3	cervix:	n/a	n/a
26	EGR1	chr3:47021812-47022345	K562	blood:	n/a	n/a
27	WRNIP1	chr3:47021770-47022416	GM12878	blood:	n/a	n/a
28	MAX	chr3:47020552-47021869	H1-hESC	embryonic stem cell:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
29	POLR2A	chr3:47020482-47021837	GM12878	blood:	n/a	n/a
30	MYC	chr3:47020489-47021844	K562	blood:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
31	MAX	chr3:47020594-47021908	ECC-1	luminal epithelium:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
32	JUN	chr3:47020315-47021981	K562	blood:	n/a	chr3:47021289-47021298 chr3:47021105-47021114
33	POLR2A	chr3:47020705-47021841	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:75185461..75186274-chr3:47021175..47021935,2	Hela-S3	cervix:
2	chr3:47020574..47023054-chr3:47051075..47053218,2	MCF-7	breast:
3	chr3:47019689..47022693-chr3:47040941..47043835,3	MCF-7	breast:
4	chr3:47019697..47022640-chr3:47324324..47326151,2	K562	blood:

Variant related genes	Relation type
CCDC12	TF binding region
ENSG00000160796	Chromatin interaction
ENSG00000236409	Chromatin interaction
ENSG00000114648	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000115350	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17784031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874265	1.00[ASN][1000 genomes]
rs1982510	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41290648	1.00[ASN][1000 genomes]
rs4683278	0.88[EUR][1000 genomes]
rs55691981	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55786350	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56121448	1.00[ASN][1000 genomes]
rs57249369	1.00[ASN][1000 genomes]
rs62246361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246376	0.87[EUR][1000 genomes]
rs62246402	0.84[EUR][1000 genomes]
rs62246404	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246409	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248895	1.00[ASN][1000 genomes]
rs62248910	1.00[ASN][1000 genomes]
rs73075647	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73079603	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
8	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases
11	esv3359860	chr3:47019973-47022521	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47020400-47022000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:47020400-47022000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:47020400-47022000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:47020400-47022200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:47020400-47022200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:47020400-47022400	Active TSS	Fetal Kidney	kidney
7	chr3:47020400-47022600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr3:47020400-47022600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:47020600-47022000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr3:47020600-47022000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:47020600-47022000	Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr3:47020600-47022000	Active TSS	Aorta	Aorta
13	chr3:47020600-47022000	Active TSS	Colon Smooth Muscle	Colon
14	chr3:47020600-47022000	Active TSS	HSMM	muscle
15	chr3:47020600-47022200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:47020600-47022200	Active TSS	Left Ventricle	heart
17	chr3:47020600-47022200	Active TSS	Right Atrium	heart
18	chr3:47020600-47022400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:47020600-47022600	Flanking Active TSS	HMEC	breast
20	chr3:47020600-47023800	Active TSS	Rectal Smooth Muscle	rectum
21	chr3:47020800-47022000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:47020800-47022000	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr3:47020800-47022000	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr3:47020800-47022000	Active TSS	Hela-S3	cervix
25	chr3:47020800-47022200	Active TSS	Brain Anterior Caudate	brain
26	chr3:47020800-47022200	Active TSS	Stomach Mucosa	stomach
27	chr3:47020800-47022400	Active TSS	Brain Substantia Nigra	brain
28	chr3:47020800-47022400	Active TSS	A549	lung
29	chr3:47021000-47022000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:47021000-47022000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:47021000-47022000	Active TSS	HepG2	liver
32	chr3:47021000-47022000	Active TSS	NHDF-Ad	bronchial
33	chr3:47021000-47022000	Active TSS	NHLF	lung
34	chr3:47021000-47022200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:47021000-47022200	Active TSS	Fetal Lung	lung
36	chr3:47021000-47022200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr3:47021000-47022400	Active TSS	Muscle Satellite Cultured Cells	--
38	chr3:47021000-47022400	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr3:47021000-47022400	Enhancers	Fetal Brain Male	brain
40	chr3:47021000-47022600	Enhancers	Fetal Heart	heart
41	chr3:47021000-47023000	Active TSS	Gastric	stomach
42	chr3:47021400-47022200	Flanking Active TSS	Liver	Liver
43	chr3:47021400-47022600	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr3:47021400-47024200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:47021600-47022000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:47021600-47022000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:47021600-47022000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:47021600-47022000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:47021600-47022000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr3:47021600-47022000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links