Variant report

Variant	rs537169993
Chromosome Location	chr12:58240259-58240260
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	MAX	chr12:58238327-58241269	K562	blood:	n/a	chr12:58239613-58239623 chr12:58238549-58238558 chr12:58238847-58238856
2	POLR2A	chr12:58238218-58240764	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:58239869-58241228	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:58238285-58241264	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr12:58238007-58241254	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:58239494-58241156	H1-neurons	neurons:	n/a	n/a
7	HCFC1	chr12:58238277-58241318	Hela-S3	cervix:	n/a	n/a
8	HEY1	chr12:58239200-58240790	HepG2	liver:	n/a	chr12:58239784-58239799 chr12:58239421-58239436 chr12:58239415-58239430
9	TAF1	chr12:58239528-58240266	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr12:58238314-58241311	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3AK20	chr12:58238035-58241331	MCF-7	breast:	n/a	n/a
12	ELF1	chr12:58238351-58241005	GM12878	blood:	n/a	chr12:58240509-58240520 chr12:58240508-58240521 chr12:58238981-58238993
13	RAD21	chr12:58239164-58241129	IMR90	lung:	n/a	chr12:58240650-58240663 chr12:58240452-58240466 chr12:58239420-58239433 chr12:58239281-58239295
14	PBX3	chr12:58239587-58240791	A549	lung:	n/a	n/a
15	MAZ	chr12:58237933-58241222	IMR90	lung:	n/a	chr12:58239613-58239623 chr12:58238549-58238558 chr12:58238847-58238856
16	POLR2A	chr12:58239273-58240677	MCF-7	breast:	n/a	n/a
17	EGR1	chr12:58239093-58240287	ECC-1	luminal epithelium:	n/a	chr12:58239610-58239623 chr12:58239611-58239620 chr12:58240010-58240019 chr12:58240003-58240025 chr12:58239614-58239624 chr12:58239611-58239622 chr12:58239215-58239229 chr12:58240007-58240020 chr12:58240008-58240022 chr12:58239609-58239624 chr12:58240009-58240019 chr12:58240007-58240021 chr12:58240010-58240020 chr12:58239610-58239623 chr12:58239592-58239606 chr12:58239219-58239228 chr12:58240006-58240021 chr12:58240009-58240019 chr12:58239610-58239623 chr12:58240007-58240020 chr12:58239609-58239623 chr12:58240007-58240020 chr12:58239610-58239623 chr12:58240007-58240020 chr12:58240008-58240019 chr12:58239607-58239621 chr12:58239595-58239608
18	ZMIZ1	chr12:58239201-58241090	K562	blood:	n/a	n/a
19	POLR2A	chr12:58239354-58241275	MCF-7	breast:	n/a	n/a
20	UBTF	chr12:58238444-58240710	K562	blood:	n/a	n/a
21	MYC	chr12:58238458-58241125	K562	blood:	n/a	chr12:58239613-58239623 chr12:58238549-58238558 chr12:58238847-58238856
22	YY1	chr12:58239891-58241096	HepG2	liver:	n/a	chr12:58240481-58240493 chr12:58240700-58240711
23	TCF7L2	chr12:58239248-58241329	HCT-116	colon:	n/a	n/a
24	MAZ	chr12:58238137-58241077	GM12878	blood:	n/a	chr12:58239613-58239623 chr12:58238549-58238558 chr12:58238847-58238856
25	NR2F2	chr12:58239051-58241153	MCF-7	breast:	n/a	n/a
26	HDAC2	chr12:58238828-58241231	MCF-7	breast:	n/a	chr12:58239481-58239490
27	FOXA2	chr12:58240162-58240940	A549	lung:	n/a	n/a
28	REST	chr12:58239088-58241136	H1-neurons	neurons:	n/a	chr12:58239380-58239390 chr12:58239593-58239606
29	CHD1	chr12:58237961-58241237	IMR90	lung:	n/a	chr12:58239243-58239253
30	HEY1	chr12:58239131-58240773	HepG2	liver:	n/a	chr12:58239784-58239799 chr12:58239421-58239436 chr12:58239415-58239430
31	POLR2A	chr12:58238203-58241217	GM19193	blood:	n/a	n/a
32	TCF12	chr12:58238829-58241303	ECC-1	luminal epithelium:	n/a	chr12:58238999-58239009 chr12:58239481-58239490 chr12:58240635-58240642 chr12:58240883-58240891
33	BCL3	chr12:58239940-58240779	A549	lung:	n/a	chr12:58240696-58240709 chr12:58240578-58240591 chr12:58240106-58240115 chr12:58240305-58240318
34	POLR2A	chr12:58239691-58241167	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr12:58239216-58241252	H1-neurons	neurons:	n/a	n/a
36	YY1	chr12:58240065-58240654	K562	blood:	n/a	chr12:58240481-58240493
37	POLR2A	chr12:58239171-58241184	U87	brain:	n/a	n/a
38	ETS1	chr12:58239225-58240262	K562	blood:	n/a	chr12:58239594-58239605 chr12:58239900-58239911 chr12:58239612-58239623
39	EP300	chr12:58238375-58241288	ECC-1	luminal epithelium:	n/a	chr12:58239274-58239283 chr12:58239481-58239491 chr12:58239790-58239806 chr12:58240681-58240697 chr12:58238989-58239005
40	SP1	chr12:58240254-58241157	H1-hESC	embryonic stem cell:	n/a	chr12:58240897-58240909 chr12:58240758-58240768 chr12:58240806-58240827 chr12:58240838-58240848 chr12:58240953-58240963 chr12:58240836-58240843 chr12:58240838-58240848 chr12:58240545-58240557 chr12:58240911-58240921 chr12:58240757-58240769 chr12:58240837-58240849 chr12:58240837-58240849 chr12:58240911-58240921 chr12:58240898-58240908 chr12:58240953-58240963 chr12:58240757-58240769 chr12:58240758-58240767 chr12:58240897-58240909 chr12:58240547-58240556 chr12:58240898-58240908
41	NFIC	chr12:58239308-58240880	ECC-1	luminal epithelium:	n/a	n/a
42	SP1	chr12:58239069-58241256	A549	lung:	n/a	chr12:58240897-58240909 chr12:58240758-58240768 chr12:58240806-58240827 chr12:58240838-58240848 chr12:58240953-58240963 chr12:58239821-58239833 chr12:58240836-58240843 chr12:58239593-58239607 chr12:58239770-58239779 chr12:58239592-58239604 chr12:58239593-58239602 chr12:58239613-58239625 chr12:58240838-58240848 chr12:58240545-58240557 chr12:58239902-58239912 chr12:58239821-58239833 chr12:58240911-58240921 chr12:58240757-58240769 chr12:58239594-58239603 chr12:58240837-58240849 chr12:58240837-58240849 chr12:58239901-58239913 chr12:58240911-58240921 chr12:58239615-58239624 chr12:58240898-58240908 chr12:58239898-58239912 chr12:58239593-58239603 chr12:58240953-58240963 chr12:58240757-58240769 chr12:58240758-58240767 chr12:58240897-58240909 chr12:58239823-58239832 chr12:58240547-58240556 chr12:58240898-58240908 chr12:58239614-58239628 chr12:58239822-58239832 chr12:58239902-58239911 chr12:58239901-58239913 chr12:58239592-58239604
43	UBTF	chr12:58238179-58240709	K562	blood:	n/a	n/a
44	PML	chr12:58238145-58241261	GM12878	blood:	n/a	n/a
45	ZBTB7A	chr12:58238713-58240797	ECC-1	luminal epithelium:	n/a	chr12:58238948-58238957 chr12:58239238-58239246 chr12:58239693-58239707
46	TBP	chr12:58238240-58241334	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:58238386-58241182	GM18526	blood:	n/a	n/a
48	POLR2A	chr12:58239162-58240740	GM12878	blood:	n/a	n/a
49	MAZ	chr12:58238463-58241190	K562	blood:	n/a	chr12:58239613-58239623 chr12:58238549-58238558 chr12:58238847-58238856
50	POLR2A	chr12:58239102-58240724	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58156406..58160029-chr12:58238044..58241191,3	MCF-7	breast:
2	chr12:58239271..58242314-chr12:58333147..58337015,4	K562	blood:
3	chr12:58164479..58167905-chr12:58237563..58242209,7	K562	blood:
4	chr12:56509109..56511870-chr12:58238772..58240512,2	MCF-7	breast:
5	chr12:58164678..58167264-chr12:58237471..58241552,5	MCF-7	breast:
6	chr12:58144944..58148202-chr12:58236897..58241575,4	MCF-7	breast:
7	chr12:58240080..58240744-chr3:33138447..33138977,2	NB4	blood:
8	chr12:58175049..58178042-chr12:58240093..58242141,3	K562	blood:
9	chr12:58176542..58178155-chr12:58239377..58241593,2	K562	blood:
10	chr12:58133058..58135797-chr12:58239105..58241667,3	MCF-7	breast:
11	chr12:58238634..58240343-chr12:58334223..58336659,2	MCF-7	breast:
12	chr12:58219695..58221744-chr12:58239321..58241689,2	MCF-7	breast:
13	chr12:58208382..58211794-chr12:58238834..58242089,3	K562	blood:
14	chr12:57997608..58000545-chr12:58238111..58240464,2	MCF-7	breast:
15	chr12:31477188..31479124-chr12:58238397..58240521,2	MCF-7	breast:
16	chr12:58162243..58164732-chr12:58237977..58240961,2	K562	blood:
17	chr12:58219013..58221062-chr12:58238426..58242369,4	K562	blood:
18	chr12:58175489..58177867-chr12:58239241..58240765,2	MCF-7	breast:
19	chr12:58212086..58214984-chr12:58238632..58241452,2	K562	blood:
20	chr12:58144058..58148099-chr12:58238749..58241436,3	K562	blood:
21	chr12:58163238..58167741-chr12:58238267..58242135,5	MCF-7	breast:
22	chr12:58236777..58241883-chr12:58327592..58331955,7	K562	blood:
23	chr12:58238134..58241883-chr12:58327269..58331955,5	K562	blood:
24	chr12:58135922..58138105-chr12:58238206..58241573,3	MCF-7	breast:
25	chr12:58236711..58242486-chr12:58286970..58293951,15	MCF-7	breast:
26	chr12:58238851..58241260-chr12:58332365..58335429,3	K562	blood:
27	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:
28	chr12:58238802..58241111-chr12:58289482..58291156,2	K562	blood:

Variant related genes	Relation type
CTDSP2	TF binding region
ENSG00000257921	Chromatin interaction
ENSG00000170266	Chromatin interaction
ENSG00000245651	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000177340	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000139146	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000166896	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000257698	Chromatin interaction
ENSG00000229117	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases
2	nsv826388	chr12:58238659-58242397	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
3	esv3415743	chr12:58239635-58241833	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58237000-58241000	Active TSS	Aorta	Aorta
2	chr12:58237200-58241200	Active TSS	Ovary	ovary
3	chr12:58237400-58241200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:58237600-58241000	Active TSS	Rectal Smooth Muscle	rectum
5	chr12:58237600-58241400	Active TSS	Brain Substantia Nigra	brain
6	chr12:58237600-58241400	Active TSS	Fetal Kidney	kidney
7	chr12:58237800-58241000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr12:58237800-58241200	Active TSS	Colon Smooth Muscle	Colon
9	chr12:58238000-58241000	Active TSS	Brain Anterior Caudate	brain
10	chr12:58238000-58241000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:58238000-58241000	Active TSS	HSMMtube	muscle
12	chr12:58238000-58241200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:58238200-58241000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr12:58238400-58240400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:58238400-58240800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:58238400-58240800	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr12:58238400-58240800	Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr12:58238400-58240800	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr12:58238400-58240800	Active TSS	Small Intestine	intestine
20	chr12:58238400-58241000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:58238400-58241000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:58238400-58241000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:58238400-58241000	Active TSS	Brain Angular Gyrus	brain
24	chr12:58238400-58241000	Active TSS	Right Ventricle	heart
25	chr12:58238400-58241000	Active TSS	Stomach Smooth Muscle	stomach
26	chr12:58238400-58241000	Active TSS	Thymus	Thymus
27	chr12:58238400-58241000	Active TSS	NHLF	lung
28	chr12:58238400-58241000	Active TSS	Osteobl	bone
29	chr12:58238400-58241200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:58238400-58241200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:58238400-58241200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr12:58238400-58241200	Active TSS	Left Ventricle	heart
33	chr12:58238400-58241200	Active TSS	NHDF-Ad	bronchial
34	chr12:58238400-58241400	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr12:58238400-58241600	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:58238400-58241800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:58238600-58240600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:58238600-58240800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:58238600-58240800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:58238600-58240800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:58238600-58240800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:58238600-58240800	Active TSS	Esophagus	oesophagus
43	chr12:58238600-58240800	Active TSS	Fetal Thymus	thymus
44	chr12:58238600-58240800	Active TSS	Gastric	stomach
45	chr12:58238600-58240800	Active TSS	Lung	lung
46	chr12:58238600-58240800	Active TSS	Placenta Amnion	Placenta Amnion
47	chr12:58238600-58240800	Active TSS	Stomach Mucosa	stomach
48	chr12:58238600-58240800	Active TSS	Spleen	Spleen
49	chr12:58238600-58241000	Active TSS	H1 Cell Line	embryonic stem cell
50	chr12:58238600-58241000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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