Variant report

Variant	rs58436504
Chromosome Location	chr12:48357188-48357189
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	CTCF	chr12:48357180-48357330	AG04449	skin:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
2	CTCF	chr12:48357100-48357250	HVMF	connective:	n/a	n/a
3	MAX	chr12:48357085-48357823	SK-N-SH	brain:	n/a	n/a
4	KAP1	chr12:48356981-48357647	HEK293	kidney:	n/a	n/a
5	MYBL2	chr12:48357103-48357527	HepG2	liver:	n/a	n/a
6	CTCF	chr12:48357160-48357310	HCM	heart:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
7	RAD21	chr12:48357011-48357539	A549	lung:	n/a	chr12:48357250-48357269
8	CTCF	chr12:48357140-48357290	GM12872	blood:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
9	TCF12	chr12:48357126-48357396	GM12878	blood:	n/a	n/a
10	CTCF	chr12:48357160-48357310	GM12865	blood:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
11	SIN3AK20	chr12:48357131-48357937	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr12:48357021-48357528	HUVEC	blood vessel:	n/a	n/a
13	HA-E2F1	chr12:48356936-48357780	MCF-7	breast:	n/a	chr12:48357366-48357375 chr12:48357371-48357380 chr12:48357333-48357347 chr12:48357367-48357374 chr12:48357322-48357331 chr12:48357393-48357402 chr12:48357443-48357452 chr12:48357366-48357377
14	POLR2A	chr12:48357134-48357600	GM12878	blood:	n/a	n/a
15	TAF1	chr12:48357147-48357634	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr12:48357120-48357401	GM10248	blood:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
17	CTCF	chr12:48357160-48357310	AG10803	skin:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
18	CTCF	chr12:48357120-48357270	GM12864	blood:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
19	CTCF	chr12:48357160-48357310	HFF	foreskin:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
20	MAZ	chr12:48357156-48357627	HepG2	liver:	n/a	n/a
21	CTCF	chr12:48357120-48357270	HFF-Myc	foreskin:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
22	CTCF	chr12:48357116-48357422	Lung_OC	lung:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
23	RAD21	chr12:48356736-48358455	SK-N-SH	brain:	n/a	chr12:48357701-48357713 chr12:48357250-48357269
24	POLR2A	chr12:48357186-48357642	Hela-S3	cervix:	n/a	n/a
25	TEAD4	chr12:48357067-48357604	HepG2	liver:	n/a	n/a
26	WRNIP1	chr12:48357116-48357668	GM12878	blood:	n/a	n/a
27	BRCA1	chr12:48357109-48357440	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr12:48357101-48357404	H1-hESC	embryonic stem cell:	n/a	chr12:48357250-48357269
29	NFIC	chr12:48357056-48358594	ECC-1	luminal epithelium:	n/a	chr12:48357541-48357557 chr12:48357540-48357557
30	CTCF	chr12:48357108-48357385	SK-N-SH_RA	brain:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
31	CTCF	chr12:48357102-48357412	NHEK	skin:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
32	CTCF	chr12:48357100-48357422	Fibrobl	skin:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
33	CBX3	chr12:48357003-48357553	K562	blood:	n/a	n/a
34	CCNT2	chr12:48357072-48357589	K562	blood:	n/a	n/a
35	FOXM1	chr12:48356993-48357484	GM12878	blood:	n/a	n/a
36	ELK4	chr12:48357154-48357461	Hela-S3	cervix:	n/a	n/a
37	RAD21	chr12:48357025-48357748	HCT-116	colon:	n/a	chr12:48357701-48357713 chr12:48357250-48357269
38	SMARCC1	chr12:48357027-48358349	Hela-S3	cervix:	n/a	n/a
39	RAD21	chr12:48357080-48357395	K562	blood:	n/a	chr12:48357250-48357269
40	SMC3	chr12:48357097-48357451	K562	blood:	n/a	n/a
41	ELF1	chr12:48357088-48357421	K562	blood:	n/a	n/a
42	YY1	chr12:48357030-48357660	GM12892	blood:	n/a	chr12:48357581-48357592
43	RUNX3	chr12:48356950-48357732	GM12878	blood:	n/a	n/a
44	MXI1	chr12:48357127-48357594	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr12:48357180-48357330	GM12873	blood:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
46	CTCF	chr12:48357140-48357290	AG04450	lung:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
47	RUNX3	chr12:48357098-48357743	GM12878	blood:	n/a	n/a
48	CTCF	chr12:48357160-48357310	Hela-S3	cervix:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270
49	SP1	chr12:48357008-48357561	A549	lung:	n/a	n/a
50	RCOR1	chr12:48357098-48357687	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48298691..48299776-chr12:48356759..48358181,8	MCF-7	breast:
2	chr12:48355845..48358792-chr12:48550018..48552863,2	K562	blood:
3	chr12:48355857..48357881-chr12:48473283..48476045,2	MCF-7	breast:
4	chr12:48297320..48300707-chr12:48356346..48358827,3	MCF-7	breast:
5	chr12:48296295..48301288-chr12:48356017..48360451,6	MCF-7	breast:

Variant related genes	Relation type
TMEM106C	TF binding region
ENSG00000111424	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000222635	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11574041	1.00[EUR][1000 genomes]
rs2525050	1.00[EUR][1000 genomes]
rs41272781	1.00[EUR][1000 genomes]
rs61048429	1.00[EUR][1000 genomes]
rs7974905	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48356600-48357200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:48356600-48357200	Flanking Active TSS	Dnd41	blood
3	chr12:48356600-48357400	Enhancers	Fetal Heart	heart
4	chr12:48356800-48357200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:48356800-48357200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr12:48356800-48357200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr12:48356800-48357200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr12:48356800-48357200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:48356800-48357200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr12:48356800-48357200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:48356800-48357200	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr12:48356800-48357200	Flanking Active TSS	Brain Cingulate Gyrus	brain
13	chr12:48356800-48357200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr12:48356800-48357200	Bivalent Enhancer	Fetal Thymus	thymus
15	chr12:48356800-48357200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr12:48356800-48357200	Flanking Active TSS	A549	lung
17	chr12:48356800-48357200	Flanking Active TSS	Hela-S3	cervix
18	chr12:48356800-48357200	Flanking Active TSS	Osteobl	bone
19	chr12:48356800-48357600	Active TSS	Brain Substantia Nigra	brain
20	chr12:48356800-48357800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:48356800-48357800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:48356800-48357800	Active TSS	Fetal Brain Female	brain
23	chr12:48356800-48358000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr12:48356800-48358000	Active TSS	Colon Smooth Muscle	Colon
25	chr12:48356800-48358000	Active TSS	Duodenum Mucosa	Duodenum
26	chr12:48356800-48358400	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr12:48357000-48357200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:48357000-48357200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:48357000-48357200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
30	chr12:48357000-48357200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:48357000-48357200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
32	chr12:48357000-48357200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
33	chr12:48357000-48357200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:48357000-48357200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
35	chr12:48357000-48357200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr12:48357000-48357200	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr12:48357000-48357200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr12:48357000-48357200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr12:48357000-48357200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr12:48357000-48357200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
41	chr12:48357000-48357200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:48357000-48357200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr12:48357000-48357200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:48357000-48357200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr12:48357000-48357200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:48357000-48357200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:48357000-48357200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr12:48357000-48357200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:48357000-48357200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:48357000-48357200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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