Variant report

Variant	rs939436
Chromosome Location	chr3:43147614-43147615
allele	C/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	NRF1	chr3:43147424-43147757	HepG2	liver:	n/a	chr3:43147529-43147543 chr3:43147569-43147580 chr3:43147569-43147583 chr3:43147532-43147546 chr3:43147566-43147580 chr3:43147571-43147580 chr3:43147569-43147580
2	CREB1	chr3:43147373-43147760	A549	lung:	n/a	n/a
3	ETS1	chr3:43147397-43147870	A549	lung:	n/a	chr3:43147636-43147649 chr3:43147408-43147419 chr3:43147405-43147416 chr3:43147411-43147422 chr3:43147635-43147648
4	POLR2A	chr3:43147303-43147734	HepG2	liver:	n/a	n/a
5	MAX	chr3:43147084-43147683	K562	blood:	n/a	chr3:43147595-43147604 chr3:43147604-43147614
6	CHD2	chr3:43147330-43147760	K562	blood:	n/a	n/a
7	TEAD4	chr3:43147354-43147984	ECC-1	luminal epithelium:	n/a	n/a
8	SMC3	chr3:43147439-43147795	K562	blood:	n/a	chr3:43147673-43147680
9	GATA1	chr3:43147303-43148051	PBDE	blood:	n/a	n/a
10	HA-E2F1	chr3:43147197-43147967	MCF-7	breast:	n/a	chr3:43147570-43147579 chr3:43147478-43147487 chr3:43147409-43147419 chr3:43147406-43147416 chr3:43147666-43147675 chr3:43147405-43147414
11	UBTF	chr3:43147265-43147622	K562	blood:	n/a	n/a
12	RFX5	chr3:43147531-43147856	HepG2	liver:	n/a	n/a
13	HA-E2F1	chr3:43147175-43147737	Hela-S3	cervix:	n/a	chr3:43147570-43147579 chr3:43147478-43147487 chr3:43147409-43147419 chr3:43147406-43147416 chr3:43147666-43147675 chr3:43147405-43147414
14	WRNIP1	chr3:43147470-43147735	GM12878	blood:	n/a	n/a
15	MAX	chr3:43146852-43147803	K562	blood:	n/a	chr3:43147595-43147604 chr3:43147604-43147614
16	JUND	chr3:43147426-43147880	K562	blood:	n/a	n/a
17	POLR2A	chr3:43147315-43147709	PANC-1	pancreas:	n/a	n/a
18	REST	chr3:43146838-43147821	H1-neurons	neurons:	n/a	chr3:43147459-43147472
19	SIX5	chr3:43147424-43147816	H1-hESC	embryonic stem cell:	n/a	chr3:43147635-43147649 chr3:43147636-43147645 chr3:43147641-43147650 chr3:43147638-43147647
20	MYC	chr3:43147478-43147853	NB4	blood:	n/a	chr3:43147595-43147604 chr3:43147604-43147614
21	CHD2	chr3:43147274-43147696	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOXA1	chr3:43147415-43147763	T-47D	breast:	n/a	n/a
23	MAX	chr3:43147073-43147805	K562	blood:	n/a	chr3:43147595-43147604 chr3:43147604-43147614
24	YY1	chr3:43147373-43147831	SK-N-SH_RA	brain:	n/a	chr3:43147666-43147675 chr3:43147405-43147416 chr3:43147476-43147490 chr3:43147409-43147423 chr3:43147387-43147396 chr3:43147664-43147678 chr3:43147411-43147420 chr3:43147405-43147414 chr3:43147381-43147395 chr3:43147478-43147487 chr3:43147408-43147417
25	MAX	chr3:43147102-43147880	HepG2	liver:	n/a	chr3:43147595-43147604 chr3:43147604-43147614
26	POLR2A	chr3:43147101-43147794	ECC-1	luminal epithelium:	n/a	n/a
27	CTCF	chr3:43147513-43147614	Kidney_OC	kidney:	n/a	n/a
28	HEY1	chr3:43147276-43147656	K562	blood:	n/a	chr3:43147550-43147565 chr3:43147545-43147560 chr3:43147379-43147394
29	CTCF	chr3:43147565-43147705	Lung_OC	lung:	n/a	chr3:43147674-43147687
30	TCF12	chr3:43147110-43147763	ECC-1	luminal epithelium:	n/a	n/a
31	E2F4	chr3:43147440-43147663	GM12878	blood:	n/a	chr3:43147570-43147579 chr3:43147478-43147487
32	MYC	chr3:43147364-43147709	MCF10A-Er-Src	breast:	n/a	chr3:43147595-43147604 chr3:43147604-43147614
33	E2F6	chr3:43147128-43147738	A549	lung:	n/a	chr3:43147570-43147579 chr3:43147478-43147487 chr3:43147396-43147407 chr3:43147409-43147419 chr3:43147406-43147416 chr3:43147666-43147675 chr3:43147405-43147414
34	MAZ	chr3:43147432-43147773	HepG2	liver:	n/a	chr3:43147595-43147604 chr3:43147604-43147614
35	POLR2A	chr3:43147294-43147701	K562	blood:	n/a	n/a
36	POLR2A	chr3:43147163-43147725	K562	blood:	n/a	n/a
37	POLR2A	chr3:43147326-43147700	A549	lung:	n/a	n/a
38	ELF1	chr3:43147457-43147735	K562	blood:	n/a	chr3:43147481-43147490
39	SIX5	chr3:43147481-43147857	K562	blood:	n/a	chr3:43147635-43147649 chr3:43147636-43147645 chr3:43147641-43147650 chr3:43147638-43147647
40	POLR2A	chr3:43147216-43147683	A549	lung:	n/a	n/a
41	TBP	chr3:43147384-43147644	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:43147417-43147659	GM12878	blood:	n/a	chr3:43147422-43147435 chr3:43147499-43147517 chr3:43147501-43147514
43	ZNF143	chr3:43147358-43147914	K562	blood:	n/a	chr3:43147638-43147647 chr3:43147629-43147647 chr3:43147624-43147643 chr3:43147636-43147645
44	POLR2A	chr3:43147184-43147819	Hela-S3	cervix:	n/a	n/a
45	CREB1	chr3:43147097-43147952	HepG2	liver:	n/a	n/a
46	POLR2A	chr3:43147265-43147707	HepG2	liver:	n/a	n/a
47	E2F6	chr3:43146716-43147760	K562	blood:	n/a	chr3:43146936-43146943 chr3:43147570-43147579 chr3:43147478-43147487 chr3:43146934-43146944 chr3:43147396-43147407 chr3:43147409-43147419 chr3:43146933-43146944 chr3:43146935-43146943 chr3:43147406-43147416 chr3:43147666-43147675 chr3:43146935-43146943 chr3:43147405-43147414
48	EP300	chr3:43147264-43147689	T-47D	breast:	n/a	chr3:43147570-43147586 chr3:43147411-43147420 chr3:43147387-43147396 chr3:43147413-43147429 chr3:43147386-43147395
49	MXI1	chr3:43147276-43147820	HepG2	liver:	n/a	n/a
50	POLR2A	chr3:43147257-43147716	Gliobla	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:43147571-43147621	CMK	blood:	n/a
2	chr3:43147571-43147621	SK-N-MC	brain:	n/a
3	chr3:43147587-43147637	HL-60	blood:	n/a
4	chr3:43147571-43147621	LNCaP	prostate:	n/a
5	chr3:43147587-43147637	H1-hESC	embryonic stem cell:	embryo
6	chr3:43147571-43147621	HEK293	kidney:	embryo
7	chr3:43147587-43147637	ProgFib	skin:	n/a
8	chr3:43147587-43147637	K562	blood:	n/a
9	chr3:43147587-43147637	ovcar-3	ovarian:	n/a
10	chr3:43147571-43147621	HCM	heart:	n/a
11	chr3:43147571-43147621	Hela-S3	cervix:	n/a
12	chr3:43147571-43147621	AG09319	gingival:	n/a
13	chr3:43147571-43147621	AG09309	skin:	n/a
14	chr3:43147587-43147637	AG09319	gingival:	n/a
15	chr3:43147571-43147621	HRCEpiC	kidney:	n/a
16	chr3:43147587-43147637	GM12878	blood:	n/a
17	chr3:43147587-43147637	CMK	blood:	n/a
18	chr3:43147587-43147637	GM19239	blood:	n/a
19	chr3:43147571-43147621	GM12878	blood:	n/a
20	chr3:43147587-43147637	HCM	heart:	n/a
21	chr3:43147587-43147637	HPAEpiC	pulmonary alveolar:	n/a
22	chr3:43147571-43147621	NT2-D1	testis:	n/a
23	chr3:43147587-43147637	PANC-1	pancreas:	n/a
24	chr3:43147587-43147637	PrEC	prostate:	n/a
25	chr3:43147587-43147637	RPTEC	kidney:	n/a
26	chr3:43147587-43147637	HUVEC	blood vessel:	n/a
27	chr3:43147587-43147637	HRCEpiC	kidney:	n/a
28	chr3:43147571-43147621	AG04449	skin:	fetal
29	chr3:43147587-43147637	NB4	blood:	n/a
30	chr3:43147571-43147621	GM06990	blood:	n/a
31	chr3:43147587-43147637	SKMC	muscle:	n/a
32	chr3:43147571-43147621	U87	brain:	n/a
33	chr3:43147571-43147621	SK-N-SH_RA	brain:	n/a
34	chr3:43147571-43147621	HUVEC	blood vessel:	n/a
35	chr3:43147587-43147637	SAEC	small airway:	n/a
36	chr3:43147587-43147637	SK-N-SH	brain:	n/a
37	chr3:43147571-43147621	AoSMC	blood vessel:	n/a
38	chr3:43147587-43147637	HIPEpiC	eye:	n/a
39	chr3:43147571-43147621	HEEpiC	esophagus:	n/a
40	chr3:43147587-43147637	NH-A	brain:	n/a
41	chr3:43147571-43147621	K562	blood:	n/a
42	chr3:43147571-43147621	HRE	kidney:	n/a
43	chr3:43147571-43147621	GM12892	blood:	n/a
44	chr3:43147587-43147637	SK-N-MC	brain:	n/a
45	chr3:43147571-43147621	PrEC	prostate:	n/a
46	chr3:43147571-43147621	MCF-7	breast:	n/a
47	chr3:43147587-43147637	MCF-7	breast:	n/a
48	chr3:43147587-43147637	Caco-2	colon:	n/a
49	chr3:43147571-43147621	PANC-1	pancreas:	n/a
50	chr3:43147587-43147637	HRE	kidney:	n/a

Variant related genes	Relation type
POMGNT2	TF binding region
POMGNT2	CpG island

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10865926	0.95[AFR][1000 genomes]
rs4683359	0.87[AFR][1000 genomes]
rs491970	0.95[AFR][1000 genomes]
rs535994	0.95[AFR][1000 genomes]
rs552472	0.95[AFR][1000 genomes]
rs632013	0.87[AFR][1000 genomes]
rs664197	0.95[AFR][1000 genomes]
rs674118	0.95[AFR][1000 genomes]
rs9828191	0.87[AFR][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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr3:43145800-43147800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:43146200-43147800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:43146200-43148000	Active TSS	HSMMtube	muscle
4	chr3:43146400-43147800	Active TSS	Fetal Kidney	kidney
5	chr3:43146400-43147800	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr3:43146400-43147800	Active TSS	HSMM	muscle
7	chr3:43146400-43147800	Active TSS	NH-A	brain
8	chr3:43146400-43148000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:43146400-43148200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:43146600-43147800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:43146600-43147800	Active TSS	Aorta	Aorta
12	chr3:43146600-43147800	Active TSS	Colonic Mucosa	Colon
13	chr3:43146600-43147800	Active TSS	NHDF-Ad	bronchial
14	chr3:43146600-43148000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:43146600-43148000	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr3:43146600-43148000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr3:43146600-43148200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr3:43146600-43148200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr3:43146600-43148200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:43146600-43148200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:43146600-43148200	Active TSS	Rectal Smooth Muscle	rectum
22	chr3:43146600-43148200	Active TSS	A549	lung
23	chr3:43146800-43147800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:43146800-43147800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:43146800-43147800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:43146800-43147800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr3:43146800-43147800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:43146800-43147800	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr3:43146800-43147800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:43146800-43147800	Active TSS	Muscle Satellite Cultured Cells	--
31	chr3:43146800-43147800	Active TSS	Brain Angular Gyrus	brain
32	chr3:43146800-43147800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr3:43146800-43147800	Active TSS	Colon Smooth Muscle	Colon
34	chr3:43146800-43147800	Active TSS	Fetal Brain Female	brain
35	chr3:43146800-43147800	Weak transcription	Fetal Heart	heart
36	chr3:43146800-43147800	Active TSS	Fetal Lung	lung
37	chr3:43146800-43147800	Active TSS	Left Ventricle	heart
38	chr3:43146800-43147800	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr3:43146800-43147800	Active TSS	Right Atrium	heart
40	chr3:43146800-43147800	Active TSS	NHLF	lung
41	chr3:43146800-43148000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr3:43146800-43148000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:43146800-43148000	Active TSS	Brain Cingulate Gyrus	brain
44	chr3:43146800-43148000	Active TSS	Brain Hippocampus Middle	brain
45	chr3:43146800-43148000	Active TSS	Brain Substantia Nigra	brain
46	chr3:43146800-43148000	Active TSS	Ovary	ovary
47	chr3:43146800-43148000	Active TSS	Stomach Mucosa	stomach
48	chr3:43146800-43148200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr3:43146800-43148200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr3:43146800-43148200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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