Variant report

Variant	rs569558305
Chromosome Location	chr15:40615485-40615486
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	CTCF	chr15:40615478-40615879	Pancreas_OC	pancreas:	n/a	chr15:40615657-40615667 chr15:40615826-40615836 chr15:40615652-40615670 chr15:40615655-40615664
2	TCF7L2	chr15:40615384-40616012	HCT-116	colon:	n/a	n/a
3	ELF1	chr15:40615301-40615964	MCF-7	breast:	n/a	chr15:40615524-40615536 chr15:40615869-40615881
4	MAX	chr15:40615224-40616200	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr15:40615181-40616130	HCT-116	colon:	n/a	n/a
6	SIN3AK20	chr15:40615093-40615953	H1-hESC	embryonic stem cell:	n/a	n/a
7	CREB1	chr15:40615334-40616100	K562	blood:	n/a	chr15:40615668-40615681 chr15:40615668-40615681
8	POLR2A	chr15:40615217-40616166	H1-neurons	neurons:	n/a	n/a
9	MAX	chr15:40615367-40615928	HUVEC	blood vessel:	n/a	n/a
10	NANOG	chr15:40615408-40615876	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr15:40615477-40615851	GM12878	blood:	n/a	chr15:40615657-40615667 chr15:40615826-40615836 chr15:40615652-40615670 chr15:40615655-40615664
12	CREB1	chr15:40615269-40616066	HepG2	liver:	n/a	chr15:40615668-40615681 chr15:40615668-40615681
13	CEBPB	chr15:40615441-40615746	H1-hESC	embryonic stem cell:	n/a	n/a
14	PBX3	chr15:40615305-40615989	SK-N-SH	brain:	n/a	n/a
15	ELF1	chr15:40615467-40615945	SK-N-SH	brain:	n/a	chr15:40615524-40615536 chr15:40615869-40615881
16	MYC	chr15:40615434-40616433	NB4	blood:	n/a	n/a
17	BCLAF1	chr15:40615405-40615906	K562	blood:	n/a	chr15:40615745-40615758 chr15:40615770-40615779 chr15:40615720-40615733 chr15:40615521-40615530 chr15:40615850-40615863
18	PBX3	chr15:40615339-40615955	SK-N-SH	brain:	n/a	n/a
19	MYBL2	chr15:40615268-40615649	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:40615310-40616160	H1-neurons	neurons:	n/a	n/a
21	JUND	chr15:40614913-40616036	SK-N-SH	brain:	n/a	n/a
22	RUNX3	chr15:40615291-40615882	GM12878	blood:	n/a	n/a
23	SIN3AK20	chr15:40615374-40615717	HepG2	liver:	n/a	n/a
24	EP300	chr15:40615336-40616086	ECC-1	luminal epithelium:	n/a	chr15:40616070-40616086 chr15:40615738-40615754 chr15:40615905-40615914 chr15:40615825-40615841 chr15:40615771-40615778 chr15:40615737-40615753
25	CHD2	chr15:40615430-40615891	H1-hESC	embryonic stem cell:	n/a	chr15:40615821-40615831 chr15:40615851-40615861 chr15:40615842-40615852
26	RCOR1	chr15:40615449-40615801	HepG2	liver:	n/a	n/a
27	CTCF	chr15:40615372-40615817	K562	blood:	n/a	chr15:40615657-40615667 chr15:40615652-40615670 chr15:40615655-40615664
28	MAX	chr15:40615398-40615928	H1-hESC	embryonic stem cell:	n/a	n/a
29	SETDB1	chr15:40615320-40615899	K562	blood:	n/a	n/a
30	SP4	chr15:40615376-40615859	H1-hESC	embryonic stem cell:	n/a	chr15:40615561-40615577 chr15:40615821-40615837
31	TCF12	chr15:40615319-40615931	ECC-1	luminal epithelium:	n/a	n/a
32	SP1	chr15:40615447-40615885	K562	blood:	n/a	chr15:40615521-40615530 chr15:40615822-40615831 chr15:40615821-40615833 chr15:40615822-40615831 chr15:40615519-40615531 chr15:40615821-40615833 chr15:40615823-40615832
33	RCOR1	chr15:40615371-40615794	Hela-S3	cervix:	n/a	n/a
34	HA-E2F1	chr15:40615443-40616266	Hela-S3	cervix:	n/a	chr15:40615823-40615832 chr15:40616080-40616090 chr15:40615820-40615832 chr15:40615747-40615757 chr15:40616077-40616087 chr15:40615523-40615532 chr15:40616070-40616080
35	SIN3AK20	chr15:40615350-40615810	HepG2	liver:	n/a	n/a
36	IRF1	chr15:40615390-40615998	K562	blood:	n/a	chr15:40615819-40615833 chr15:40615519-40615533
37	MAX	chr15:40615314-40616070	SK-N-SH	brain:	n/a	n/a
38	MAZ	chr15:40615386-40615985	HepG2	liver:	n/a	n/a
39	CTCF	chr15:40615451-40615924	Spleen_OC	spleen:	n/a	chr15:40615657-40615667 chr15:40615826-40615836 chr15:40615652-40615670 chr15:40615655-40615664
40	MYC	chr15:40615263-40615825	H1-hESC	embryonic stem cell:	n/a	n/a
41	SP4	chr15:40615427-40615885	H1-hESC	embryonic stem cell:	n/a	chr15:40615561-40615577 chr15:40615821-40615837
42	CTCF	chr15:40615485-40615767	GM12891	blood:	n/a	chr15:40615657-40615667 chr15:40615652-40615670 chr15:40615655-40615664
43	E2F6	chr15:40615438-40615913	A549	lung:	n/a	chr15:40615823-40615832 chr15:40615820-40615832 chr15:40615747-40615757 chr15:40615881-40615896 chr15:40615523-40615532
44	UBTF	chr15:40615366-40616866	K562	blood:	n/a	n/a
45	JUND	chr15:40615075-40616552	GM12878	blood:	n/a	chr15:40616113-40616122 chr15:40616478-40616487
46	JUN	chr15:40614979-40616024	K562	blood:	n/a	n/a
47	RAD21	chr15:40615434-40615826	H1-hESC	embryonic stem cell:	n/a	chr15:40615803-40615816 chr15:40615653-40615672
48	REST	chr15:40615464-40615688	K562	blood:	n/a	n/a
49	SP1	chr15:40615384-40615918	A549	lung:	n/a	chr15:40615521-40615530 chr15:40615822-40615831 chr15:40615821-40615833 chr15:40615822-40615831 chr15:40615519-40615531 chr15:40615821-40615833 chr15:40615823-40615832
50	SIN3AK20	chr15:40615285-40616201	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40615161..40616254-chr15:40713827..40714847,4	K562	blood:
2	chr15:40614221..40619136-chr15:40629898..40635011,9	K562	blood:
3	chr15:40583616..40585723-chr15:40614548..40617090,2	K562	blood:
4	chr15:40573745..40575892-chr15:40613923..40616158,2	K562	blood:
5	chr15:40607352..40610567-chr15:40611377..40615529,4	MCF-7	breast:
6	chr15:40606578..40610704-chr15:40612489..40616999,9	K562	blood:
7	chr15:40581922..40583593-chr15:40614518..40616173,2	K562	blood:
8	chr15:40596957..40600729-chr15:40613519..40617071,4	K562	blood:
9	chr15:40615118..40617051-chr15:40729542..40732021,2	K562	blood:
10	chr15:40613571..40616194-chr15:40676591..40679577,2	K562	blood:
11	chr15:40614961..40616867-chr15:40712396..40714190,2	MCF-7	breast:
12	chr15:40611920..40613859-chr15:40613927..40615590,2	K562	blood:
13	chr15:40573791..40575924-chr15:40613554..40617283,3	MCF-7	breast:
14	chr15:40608873..40611853-chr15:40613878..40616202,2	MCF-7	breast:
15	chr15:40510541..40512947-chr15:40613762..40616049,2	K562	blood:
16	chr15:40606578..40609257-chr15:40612890..40617072,4	K562	blood:
17	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
18	chr15:40599147..40601689-chr15:40614013..40619011,4	K562	blood:
19	chr15:40613324..40616013-chr15:40714259..40715828,2	K562	blood:
20	chr15:40613668..40617143-chr15:40761466..40764045,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf52-1	chr15:40615444-40615570	XLOC_011441

Variant related genes	Relation type
LINC00984	TF binding region
ENSG00000140320	Chromatin interaction
ENSG00000259288	Chromatin interaction
ENSG00000230778	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000169105	Chromatin interaction
ENSG00000188549	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv827305	chr15:40596162-40625922	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3378883	chr15:40614885-40617433	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3428901	chr15:40615210-40617508	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3438791	chr15:40615285-40617833	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr15:40612400-40615600	Enhancers	Fetal Heart	heart
2	chr15:40613400-40617000	Enhancers	Fetal Brain Male	brain
3	chr15:40614200-40615600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:40614600-40615600	Enhancers	Lung	lung
5	chr15:40614600-40615600	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr15:40614600-40615600	Flanking Active TSS	NHEK	skin
7	chr15:40614800-40615600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:40614800-40615600	Enhancers	Stomach Mucosa	stomach
9	chr15:40614800-40616800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr15:40614800-40617000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr15:40614800-40617200	Active TSS	Gastric	stomach
12	chr15:40614800-40618200	Active TSS	Colon Smooth Muscle	Colon
13	chr15:40614800-40618400	Active TSS	Aorta	Aorta
14	chr15:40615000-40615600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr15:40615000-40615600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:40615000-40615600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:40615000-40615600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr15:40615000-40615600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr15:40615000-40615600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr15:40615000-40615600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr15:40615000-40615600	Flanking Active TSS	Colonic Mucosa	Colon
22	chr15:40615000-40615600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
23	chr15:40615000-40615600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr15:40615000-40615600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr15:40615000-40615600	Flanking Active TSS	Dnd41	blood
26	chr15:40615000-40615600	Flanking Active TSS	HSMM	muscle
27	chr15:40615000-40615600	Enhancers	HUVEC	blood vessel
28	chr15:40615000-40615600	Flanking Active TSS	Osteobl	bone
29	chr15:40615000-40615800	Enhancers	Primary hematopoietic stem cells	blood
30	chr15:40615000-40615800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:40615000-40616800	Active TSS	Brain Angular Gyrus	brain
32	chr15:40615000-40616800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:40615000-40617000	Active TSS	Brain Anterior Caudate	brain
34	chr15:40615000-40617000	Active TSS	Brain Cingulate Gyrus	brain
35	chr15:40615000-40617200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:40615200-40615600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:40615200-40615600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:40615200-40615600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr15:40615200-40615600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:40615200-40615600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr15:40615200-40615600	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr15:40615200-40615600	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr15:40615200-40615600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr15:40615200-40615600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:40615200-40615600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr15:40615200-40615600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr15:40615200-40615600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr15:40615200-40615600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:40615200-40615600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr15:40615200-40615600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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