Variant report

Variant	rs139725139
Chromosome Location	chr15:72765746-72765747
allele	C/T
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	POLR2A	chr15:72765737-72766951	SK-N-SH	brain:	n/a	n/a
2	BCL3	chr15:72765450-72767786	A549	lung:	n/a	chr15:72767688-72767697 chr15:72766587-72766600 chr15:72767366-72767375
3	IRF1	chr15:72765670-72766919	K562	blood:	n/a	n/a
4	TAL1	chr15:72765477-72767094	K562	blood:	n/a	n/a
5	BHLHE40	chr15:72765602-72766850	GM12878	blood:	n/a	chr15:72766718-72766734
6	GATA3	chr15:72765698-72767958	A549	lung:	n/a	n/a
7	POLR2A	chr15:72765298-72767176	SK-N-MC	brain:	n/a	n/a
8	MAX	chr15:72765355-72768226	A549	lung:	n/a	n/a
9	JUND	chr15:72765340-72768137	SK-N-SH	brain:	n/a	chr15:72766104-72766113 chr15:72766289-72766298
10	MTA3	chr15:72765400-72766891	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:72765485-72768004	Hela-S3	cervix:	n/a	n/a
12	FOXA2	chr15:72765664-72767063	A549	lung:	n/a	n/a
13	FOSL2	chr15:72765237-72766903	A549	lung:	n/a	chr15:72766104-72766113 chr15:72766289-72766298
14	POLR2A	chr15:72765560-72766946	HepG2	liver:	n/a	n/a
15	CTCF	chr15:72765620-72765770	AoAF	blood vessel:	n/a	n/a
16	POLR2A	chr15:72765344-72767200	GM12892	blood:	n/a	n/a
17	SP1	chr15:72765464-72767009	A549	lung:	n/a	chr15:72766591-72766600 chr15:72766655-72766662 chr15:72766590-72766602 chr15:72766590-72766601 chr15:72766591-72766601 chr15:72766590-72766602 chr15:72766592-72766601 chr15:72766592-72766601
18	CTCF	chr15:72765620-72765770	AG09319	gingival:	n/a	n/a
19	RFX5	chr15:72765740-72766715	K562	blood:	n/a	chr15:72766230-72766245 chr15:72766230-72766245 chr15:72766229-72766246 chr15:72766230-72766245
20	FOS	chr15:72765666-72766759	HUVEC	blood vessel:	n/a	chr15:72766104-72766113 chr15:72766289-72766298
21	POLR2A	chr15:72765551-72768027	GM18505	blood:	n/a	n/a
22	ELF1	chr15:72765727-72766940	HCT-116	colon:	n/a	chr15:72766269-72766280 chr15:72766268-72766281 chr15:72766270-72766279
23	POLR2A	chr15:72765528-72767906	HUVEC	blood vessel:	n/a	n/a
24	REST	chr15:72765139-72768413	H1-neurons	neurons:	n/a	chr15:72767437-72767450 chr15:72767437-72767450 chr15:72767557-72767570
25	ELK1	chr15:72765734-72766710	K562	blood:	n/a	n/a
26	ELF1	chr15:72765676-72766824	A549	lung:	n/a	chr15:72766269-72766280 chr15:72766268-72766281 chr15:72766270-72766279
27	SIN3A	chr15:72765676-72768269	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr15:72765451-72767953	MCF-7	breast:	n/a	n/a
29	POLR2A	chr15:72765417-72768122	IMR90	lung:	n/a	n/a
30	POLR2A	chr15:72765345-72767924	GM12892	blood:	n/a	n/a
31	NFIC	chr15:72765641-72766755	GM12878	blood:	n/a	n/a
32	POLR2A	chr15:72765486-72766869	HepG2	liver:	n/a	n/a
33	POLR2A	chr15:72765365-72768126	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr15:72765264-72768062	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr15:72765392-72768142	GM12878	blood:	n/a	n/a
36	IRF1	chr15:72765669-72766857	K562	blood:	n/a	n/a
37	POLR2A	chr15:72765313-72768094	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr15:72765390-72767182	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr15:72765420-72768235	HepG2	liver:	n/a	n/a
40	ATF2	chr15:72765717-72766773	H1-hESC	embryonic stem cell:	n/a	chr15:72766643-72766657
41	MAZ	chr15:72765720-72767071	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:72765438-72766972	K562	blood:	n/a	n/a
43	POLR2A	chr15:72765413-72767160	U87	brain:	n/a	n/a
44	JUN	chr15:72765673-72766368	Hela-S3	cervix:	n/a	chr15:72766104-72766113 chr15:72766289-72766298 chr15:72766100-72766113
45	SIX5	chr15:72765520-72766851	A549	lung:	n/a	n/a
46	POLR2A	chr15:72765460-72767084	K562	blood:	n/a	n/a
47	POLR2A	chr15:72765472-72768175	A549	lung:	n/a	n/a
48	BRCA1	chr15:72765743-72766810	Hela-S3	cervix:	n/a	chr15:72766241-72766248
49	KAP1	chr15:72765695-72766689	HEK293	kidney:	n/a	n/a
50	ATF3	chr15:72765720-72766864	A549	lung:	n/a	chr15:72766594-72766614 chr15:72766105-72766112 chr15:72766104-72766112 chr15:72766105-72766113 chr15:72766646-72766660 chr15:72766620-72766640 chr15:72766101-72766116

No.	Distal block	Cell Line	Cell type
1	chr15:72750881..72760234-chr15:72764528..72769120,23	MCF-7	breast:
2	chr15:72765683..72767705-chr9:134393823..134395690,2	MCF-7	breast:
3	chr15:72692001..72694745-chr15:72764264..72766502,3	MCF-7	breast:
4	chr15:72497804..72499839-chr15:72765083..72768033,2	K562	blood:
5	chr15:72666558..72670735-chr15:72765041..72769475,12	MCF-7	breast:
6	chr15:72765203..72766825-chr15:73342381..73345092,2	MCF-7	breast:
7	chr15:72458549..72461101-chr15:72765178..72767894,2	K562	blood:
8	chr15:72666408..72669827-chr15:72764535..72767754,3	MCF-7	breast:
9	chr15:72520897..72524301-chr15:72765072..72768298,5	K562	blood:
10	chr15:72667344..72672450-chr15:72764755..72768100,8	K562	blood:
11	chr15:72609440..72614186-chr15:72765313..72769259,6	MCF-7	breast:
12	chr15:72765119..72766854-chr2:171784790..171787087,2	K562	blood:
13	chr15:72742962..72745809-chr15:72764358..72766379,2	MCF-7	breast:
14	chr15:72764026..72766932-chr15:72877151..72879938,2	K562	blood:
15	chr15:72764850..72767674-chr15:72977020..72979928,5	K562	blood:
16	chr15:72765370..72766302-chr5:43313191..43314042,2	Hela-S3	cervix:
17	chr15:72765649..72767573-chr15:72851905..72854681,2	MCF-7	breast:
18	chr15:72476533..72478146-chr15:72764010..72766539,2	MCF-7	breast:
19	chr15:72649215..72653843-chr15:72765321..72768285,4	MCF-7	breast:
20	chr15:72523282..72524844-chr15:72764635..72767200,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HEXA-3	chr15:72761633-72766666	NONHSAT047096

Variant related genes	Relation type
ARIH1	TF binding region
ENSG00000273025	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000271072	Chromatin interaction
ENSG00000207690	Chromatin interaction
ENSG00000261187	Chromatin interaction
ENSG00000130714	Chromatin interaction
ENSG00000213614	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000140488	Chromatin interaction
ENSG00000243007	Chromatin interaction
ENSG00000260729	Chromatin interaction
ENSG00000175318	Chromatin interaction
ENSG00000115806	Chromatin interaction
ENSG00000175202	Chromatin interaction
ENSG00000260339	Chromatin interaction
ENSG00000112972	Chromatin interaction
ENSG00000140463	Chromatin interaction
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
3	nsv534037	chr15:72659210-72964029	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv469704	chr15:72669374-72853927	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
5	nsv482685	chr15:72669374-72853927	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv1050558	chr15:72739150-72860350	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
7	nsv542427	chr15:72739150-72860350	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
8	nsv827384	chr15:72765222-72768609	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72755000-72766000	Weak transcription	Ovary	ovary
2	chr15:72761000-72766200	Weak transcription	Small Intestine	intestine
3	chr15:72765200-72765800	Flanking Active TSS	A549	lung
4	chr15:72765200-72766000	Flanking Active TSS	Hela-S3	cervix
5	chr15:72765400-72765800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:72765400-72765800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:72765400-72765800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:72765400-72765800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr15:72765400-72765800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:72765400-72765800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr15:72765400-72765800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr15:72765400-72765800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:72765400-72765800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:72765400-72765800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:72765400-72765800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr15:72765400-72765800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:72765400-72765800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:72765400-72765800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:72765400-72765800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:72765400-72765800	Flanking Active TSS	Liver	Liver
21	chr15:72765400-72765800	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr15:72765400-72765800	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr15:72765400-72765800	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr15:72765400-72765800	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr15:72765400-72765800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:72765400-72765800	Flanking Active TSS	Colonic Mucosa	Colon
27	chr15:72765400-72765800	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr15:72765400-72765800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr15:72765400-72765800	Flanking Active TSS	Fetal Lung	lung
30	chr15:72765400-72765800	Enhancers	Placenta	Placenta
31	chr15:72765400-72765800	Enhancers	Fetal Thymus	thymus
32	chr15:72765400-72765800	Enhancers	Pancreas	Pancrea
33	chr15:72765400-72765800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr15:72765400-72765800	Flanking Active TSS	Psoas Muscle	Psoas
35	chr15:72765400-72765800	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr15:72765400-72765800	Flanking Active TSS	Right Atrium	heart
37	chr15:72765400-72765800	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr15:72765400-72765800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr15:72765400-72765800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr15:72765400-72765800	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr15:72765400-72765800	Enhancers	Spleen	Spleen
42	chr15:72765400-72765800	Flanking Active TSS	GM12878-XiMat	blood
43	chr15:72765400-72765800	Flanking Bivalent TSS/Enh	HepG2	liver
44	chr15:72765400-72765800	Flanking Active TSS	K562	blood
45	chr15:72765400-72766000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:72765400-72766000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:72765400-72766000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr15:72765400-72766000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr15:72765400-72766000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:72765400-72766000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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