Variant report

Variant	rs2440317
Chromosome Location	chr15:53082471-53082472
allele	A/C
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	chr15:53082246-53082979	SK-N-SH	brain:	n/a	chr15:53082611-53082625 chr15:53082613-53082622 chr15:53082611-53082622 chr15:53082631-53082640 chr15:53082608-53082622 chr15:53082611-53082620
2	POLR2A	chr15:53082401-53082857	HepG2	liver:	n/a	n/a
3	EP300	chr15:53082381-53082815	ECC-1	luminal epithelium:	n/a	chr15:53082769-53082778
4	E2F6	chr15:53082432-53082920	A549	lung:	n/a	chr15:53082631-53082640 chr15:53082612-53082621 chr15:53082625-53082634
5	MAX	chr15:53081889-53083046	ECC-1	luminal epithelium:	n/a	chr15:53082734-53082745
6	POLR2A	chr15:53082426-53082787	A549	lung:	n/a	n/a
7	MAX	chr15:53082463-53083020	H1-hESC	embryonic stem cell:	n/a	chr15:53082734-53082745
8	EGR1	chr15:53082433-53082840	H1-hESC	embryonic stem cell:	n/a	chr15:53082626-53082639 chr15:53082626-53082636 chr15:53082625-53082639 chr15:53082585-53082598 chr15:53082623-53082637 chr15:53082626-53082639 chr15:53082626-53082639 chr15:53082612-53082621 chr15:53082626-53082639 chr15:53082627-53082636 chr15:53082630-53082640 chr15:53082625-53082640
9	POLR2A	chr15:53082422-53082904	A549	lung:	n/a	n/a
10	SIN3A	chr15:53082212-53082957	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr15:53082428-53082967	Gliobla	brain:	n/a	n/a
12	POLR2A	chr15:53082419-53082838	A549	lung:	n/a	n/a
13	POLR2A	chr15:53082355-53082650	HCT-116	colon:	n/a	n/a
14	MAX	chr15:53081564-53083062	MCF-7	breast:	n/a	chr15:53082734-53082745
15	E2F6	chr15:53082389-53082813	K562	blood:	n/a	chr15:53082631-53082640 chr15:53082612-53082621 chr15:53082625-53082634
16	POLR2A	chr15:53082035-53082889	MCF-7	breast:	n/a	n/a
17	MAX	chr15:53082151-53082945	NB4	blood:	n/a	chr15:53082734-53082745
18	MXI1	chr15:53081885-53082891	HepG2	liver:	n/a	n/a
19	EGR1	chr15:53082419-53082996	MCF-7	breast:	n/a	chr15:53082626-53082639 chr15:53082626-53082636 chr15:53082625-53082639 chr15:53082585-53082598 chr15:53082623-53082637 chr15:53082626-53082639 chr15:53082626-53082639 chr15:53082612-53082621 chr15:53082626-53082639 chr15:53082627-53082636 chr15:53082630-53082640 chr15:53082625-53082640
20	TAF1	chr15:53082334-53082826	HepG2	liver:	n/a	n/a
21	POLR2A	chr15:53081890-53082920	HepG2	liver:	n/a	n/a
22	BHLHE40	chr15:53082092-53082932	HepG2	liver:	n/a	chr15:53082735-53082744 chr15:53082735-53082744 chr15:53082462-53082478 chr15:53082455-53082471 chr15:53082734-53082743
23	MAX	chr15:53082447-53083017	ECC-1	luminal epithelium:	n/a	chr15:53082734-53082745
24	CEBPD	chr15:53082328-53082849	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:53082227-53082949	ProgFib	skin:	n/a	n/a
26	TAF1	chr15:53082353-53082902	HepG2	liver:	n/a	n/a
27	REST	chr15:53081961-53083143	H1-neurons	neurons:	n/a	chr15:53082722-53082732 chr15:53083002-53083012 chr15:53082831-53082840 chr15:53082943-53082953
28	POLR2A	chr15:53081925-53082886	HepG2	liver:	n/a	n/a
29	CCNT2	chr15:53082422-53082718	K562	blood:	n/a	chr15:53082631-53082640
30	POLR2A	chr15:53082079-53082826	HepG2	liver:	n/a	n/a
31	POLR2A	chr15:53082205-53082870	MCF-7	breast:	n/a	n/a
32	E2F6	chr15:53082383-53082992	A549	lung:	n/a	chr15:53082631-53082640 chr15:53082612-53082621 chr15:53082625-53082634
33	POLR2A	chr15:53081468-53083469	H1-neurons	neurons:	n/a	n/a
34	NRF1	chr15:53082426-53082803	GM12878	blood:	n/a	chr15:53082611-53082625 chr15:53082613-53082622 chr15:53082611-53082622 chr15:53082631-53082640 chr15:53082608-53082622 chr15:53082611-53082620
35	CREB1	chr15:53082304-53082856	A549	lung:	n/a	n/a
36	POLR2A	chr15:53082331-53082936	Raji	blood:	n/a	n/a
37	POLR2A	chr15:53081618-53082970	HepG2	liver:	n/a	n/a
38	CHD1	chr15:53082377-53082521	H1-hESC	embryonic stem cell:	n/a	chr15:53082489-53082499
39	ARID3A	chr15:53082218-53082726	HepG2	liver:	n/a	n/a
40	HA-E2F1	chr15:53081797-53083000	MCF-7	breast:	n/a	chr15:53082631-53082640 chr15:53082612-53082621 chr15:53082625-53082634
41	POLR2A	chr15:53082351-53082831	MCF-7	breast:	n/a	n/a
42	YY1	chr15:53081690-53082916	HepG2	liver:	n/a	chr15:53082450-53082461 chr15:53082628-53082639 chr15:53082631-53082640 chr15:53082487-53082501 chr15:53082625-53082639 chr15:53082468-53082479 chr15:53082628-53082637 chr15:53082471-53082485
43	MAX	chr15:53081725-53083169	MCF-7	breast:	n/a	chr15:53082734-53082745
44	HEY1	chr15:53082003-53082891	HepG2	liver:	n/a	chr15:53082464-53082479 chr15:53082449-53082464 chr15:53082735-53082744 chr15:53082647-53082662 chr15:53082624-53082639
45	MAX	chr15:53081737-53083149	A549	lung:	n/a	chr15:53082734-53082745
46	CTBP2	chr15:53079913-53083729	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr15:53082354-53082951	A549	lung:	n/a	n/a
48	POLR2A	chr15:53082366-53082832	HCT-116	colon:	n/a	n/a
49	NRF1	chr15:53082429-53082818	H1-hESC	embryonic stem cell:	n/a	chr15:53082611-53082625 chr15:53082613-53082622 chr15:53082611-53082622 chr15:53082631-53082640 chr15:53082608-53082622 chr15:53082611-53082620
50	POLR2A	chr15:53081582-53083054	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:53072756..53074429-chr15:53080987..53082654,2	MCF-7	breast:
2	chr15:53072465..53075963-chr15:53080706..53083147,3	MCF-7	breast:

Variant related genes	Relation type
ONECUT1	TF binding region
ENSG00000169856	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10518694	0.85[ASN][1000 genomes]
rs2440322	0.84[ASN][1000 genomes]
rs2456507	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2456522	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2456524	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2456526	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28475375	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv457142	chr15:53041887-53091896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	nsv569427	chr15:53041887-53091896	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
5	nsv1046970	chr15:53065114-53142386	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	nsv569428	chr15:53069874-53140045	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53075600-53083600	Bivalent Enhancer	Fetal Brain Male	brain
2	chr15:53076400-53083800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr15:53080600-53083800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr15:53081000-53083000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
5	chr15:53081200-53083000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chr15:53081200-53083200	Active TSS	HepG2	liver
7	chr15:53081200-53083800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr15:53081200-53083800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr15:53081400-53082600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
10	chr15:53081400-53083400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:53081400-53083400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:53081400-53083400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
13	chr15:53081600-53082800	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr15:53081600-53083000	Flanking Active TSS	Dnd41	blood
15	chr15:53081600-53083000	Bivalent/Poised TSS	HSMMtube	muscle
16	chr15:53081600-53083400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
17	chr15:53081600-53083400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:53081600-53083600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:53081600-53083600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:53081600-53083800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
21	chr15:53081600-53083800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:53081600-53083800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
23	chr15:53081800-53082600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:53081800-53082800	Active TSS	Right Atrium	heart
25	chr15:53081800-53082800	Bivalent/Poised TSS	NHEK	skin
26	chr15:53081800-53083000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:53081800-53083000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:53081800-53083000	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr15:53081800-53083200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr15:53081800-53083400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:53081800-53083400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
32	chr15:53081800-53083600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
33	chr15:53081800-53083600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:53081800-53083800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:53081800-53083800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr15:53081800-53084000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:53082000-53082800	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:53082000-53083000	Active TSS	A549	lung
39	chr15:53082000-53083000	Active TSS	HSMM	muscle
40	chr15:53082000-53083000	Active TSS	K562	blood
41	chr15:53082000-53083000	Active TSS	NHDF-Ad	bronchial
42	chr15:53082000-53083200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:53082000-53083200	Bivalent/Poised TSS	Psoas Muscle	Psoas
44	chr15:53082000-53083200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
45	chr15:53082000-53083400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr15:53082000-53083400	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:53082000-53083400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
48	chr15:53082000-53083600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
49	chr15:53082000-53083600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
50	chr15:53082000-53083800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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