Variant report

Variant	rs530078594
Chromosome Location	chr12:50101408-50101409
allele	-/CGGCC
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	chr12:50101139-50101898	MCF-7	breast:	n/a	chr12:50101498-50101516
2	FOXP2	chr12:50101032-50101577	PFSK-1	brain:	n/a	n/a
3	CTCF	chr12:50101164-50101720	GM12878	blood:	n/a	chr12:50101498-50101516
4	TBP	chr12:50101143-50101640	K562	blood:	n/a	n/a
5	MEF2A	chr12:50101040-50101704	GM12878	blood:	n/a	n/a
6	USF1	chr12:50101248-50101561	A549	lung:	n/a	n/a
7	PML	chr12:50100681-50101899	GM12878	blood:	n/a	n/a
8	POU2F2	chr12:50101099-50101609	GM12891	blood:	n/a	chr12:50101117-50101129 chr12:50101380-50101392 chr12:50101418-50101430
9	EP300	chr12:50101267-50101650	K562	blood:	n/a	chr12:50101414-50101430
10	CTCF	chr12:50101278-50101644	GM13976	blood:	n/a	chr12:50101498-50101516
11	MAZ	chr12:50101280-50101554	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:50101218-50101583	HCT-116	colon:	n/a	n/a
13	GTF2F1	chr12:50101331-50101672	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr12:50100944-50101611	GM12878	blood:	n/a	chr12:50101407-50101421 chr12:50101556-50101567 chr12:50101378-50101392 chr12:50101114-50101128 chr12:50101120-50101129 chr12:50101416-50101430
15	E2F6	chr12:50100838-50102015	K562	blood:	n/a	chr12:50101123-50101132 chr12:50101375-50101385 chr12:50101380-50101389 chr12:50101463-50101474
16	GATA3	chr12:50101279-50101653	T-47D	breast:	n/a	n/a
17	SP1	chr12:50101215-50101709	HepG2	liver:	n/a	chr12:50101414-50101425 chr12:50101378-50101390 chr12:50101465-50101476 chr12:50101380-50101389 chr12:50101379-50101388 chr12:50101378-50101390 chr12:50101379-50101393 chr12:50101415-50101424
18	CTCF	chr12:50101271-50101752	MCF-7	breast:	n/a	chr12:50101498-50101516
19	ZBTB33	chr12:50101266-50101683	HCT-116	colon:	n/a	n/a
20	POLR2A	chr12:50101076-50101432	A549	lung:	n/a	n/a
21	RCOR1	chr12:50100984-50101654	K562	blood:	n/a	n/a
22	MAX	chr12:50100796-50101873	K562	blood:	n/a	n/a
23	CTCF	chr12:50101351-50101616	HepG2	liver:	n/a	chr12:50101498-50101516
24	YY1	chr12:50101189-50101613	HCT-116	colon:	n/a	chr12:50101407-50101421 chr12:50101556-50101567 chr12:50101378-50101392 chr12:50101416-50101430
25	CTCF	chr12:50101237-50101778	A549	lung:	n/a	chr12:50101498-50101516
26	POLR2A	chr12:50100851-50101509	GM15510	blood:	n/a	n/a
27	HDAC2	chr12:50101129-50101557	K562	blood:	n/a	n/a
28	RAD21	chr12:50101311-50101686	A549	lung:	n/a	n/a
29	E2F6	chr12:50100984-50101665	K562	blood:	n/a	chr12:50101123-50101132 chr12:50101375-50101385 chr12:50101380-50101389 chr12:50101463-50101474
30	JUND	chr12:50101342-50101705	H1-hESC	embryonic stem cell:	n/a	chr12:50101381-50101390 chr12:50101452-50101461
31	USF1	chr12:50101241-50101723	ECC-1	luminal epithelium:	n/a	n/a
32	NFYA	chr12:50101226-50101871	Hela-S3	cervix:	n/a	chr12:50101448-50101461 chr12:50101448-50101466
33	CTCF	chr12:50101298-50101640	Hela-S3	cervix:	n/a	chr12:50101498-50101516
34	RAD21	chr12:50100941-50101802	IMR90	lung:	n/a	n/a
35	POLR2A	chr12:50101023-50101450	A549	lung:	n/a	n/a
36	RELA	chr12:50100937-50101773	GM19099	blood:	n/a	n/a
37	CTCF	chr12:50101346-50101635	GM20000	blood:	n/a	chr12:50101498-50101516
38	MAX	chr12:50100931-50101876	MCF-7	breast:	n/a	n/a
39	TAF1	chr12:50101133-50101559	SK-N-SH	brain:	n/a	n/a
40	USF1	chr12:50101271-50101592	SK-N-SH_RA	brain:	n/a	n/a
41	ZC3H11A	chr12:50101358-50101735	K562	blood:	n/a	n/a
42	ZEB1	chr12:50100927-50101548	GM12878	blood:	n/a	n/a
43	YY1	chr12:50100759-50101660	GM12878	blood:	n/a	chr12:50101407-50101421 chr12:50101556-50101567 chr12:50101378-50101392 chr12:50101114-50101128 chr12:50101120-50101129 chr12:50101416-50101430
44	SP2	chr12:50101265-50101632	K562	blood:	n/a	chr12:50101414-50101429 chr12:50101434-50101457 chr12:50101465-50101480 chr12:50101436-50101459
45	RAD21	chr12:50101178-50101812	A549	lung:	n/a	n/a
46	POLR2A	chr12:50100916-50101543	K562	blood:	n/a	n/a
47	POLR2A	chr12:50100980-50101476	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr12:50101340-50101490	GM12870	blood:	n/a	n/a
49	CTCF	chr12:50101194-50101646	GM19239	blood:	n/a	chr12:50101498-50101516
50	GABPA	chr12:50100818-50101643	K562	blood:	n/a	chr12:50101127-50101136 chr12:50101412-50101421

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:50101363-50101413	RPTEC	kidney:	n/a
2	chr12:50101363-50101413	MCF10A-Er-Src	breast:	n/a
3	chr12:50101359-50101409	SK-N-MC	brain:	n/a
4	chr12:50101363-50101413	HCPEpiC	choroid plexus:	n/a
5	chr12:50101363-50101413	GM12878	blood:	n/a
6	chr12:50101363-50101413	LNCaP	prostate:	n/a
7	chr12:50101359-50101409	HMEC	breast:	n/a
8	chr12:50101359-50101409	HAEpiC	amniotic membrane:	n/a
9	chr12:50101359-50101409	K562	blood:	n/a
10	chr12:50101359-50101409	CMK	blood:	n/a
11	chr12:50101363-50101413	HL-60	blood:	n/a
12	chr12:50101359-50101409	HEEpiC	esophagus:	n/a
13	chr12:50101363-50101413	U87	brain:	n/a
14	chr12:50101359-50101409	HRE	kidney:	n/a
15	chr12:50101363-50101413	NHBE	bronchial:	n/a
16	chr12:50101363-50101413	GM12891	blood:	n/a
17	chr12:50101363-50101413	GM12892	blood:	n/a
18	chr12:50101359-50101409	AG10803	skin:	n/a
19	chr12:50101363-50101413	NT2-D1	testis:	n/a
20	chr12:50101363-50101413	HMEC	breast:	n/a
21	chr12:50101359-50101409	NHDF-neo	bronchial:	n/a
22	chr12:50101359-50101409	HCT-116	colon:	n/a
23	chr12:50101363-50101413	AG04449	skin:	fetal
24	chr12:50101363-50101413	Caco-2	colon:	n/a
25	chr12:50101363-50101413	AoSMC	blood vessel:	n/a
26	chr12:50101359-50101409	AG04449	skin:	fetal
27	chr12:50101363-50101413	Hela-S3	cervix:	n/a
28	chr12:50101363-50101413	NHDF-neo	bronchial:	n/a
29	chr12:50101363-50101413	HCT-116	colon:	n/a
30	chr12:50101359-50101409	GM19239	blood:	n/a
31	chr12:50101363-50101413	HNPCEpiC	eye:	n/a
32	chr12:50101363-50101413	HepG2	liver:	n/a
33	chr12:50101359-50101409	NHBE	bronchial:	n/a
34	chr12:50101359-50101409	HepG2	liver:	n/a
35	chr12:50101359-50101409	HCF	heart:	n/a
36	chr12:50101359-50101409	AG04450	lung:	fetal
37	chr12:50101359-50101409	A549	lung:	n/a
38	chr12:50101359-50101409	SKMC	muscle:	n/a
39	chr12:50101363-50101413	HRCEpiC	kidney:	n/a
40	chr12:50101363-50101413	H1-hESC	embryonic stem cell:	embryo
41	chr12:50101363-50101413	GM19239	blood:	n/a
42	chr12:50101363-50101413	HPAEpiC	pulmonary alveolar:	n/a
43	chr12:50101359-50101409	HIPEpiC	eye:	n/a
44	chr12:50101359-50101409	NB4	blood:	n/a
45	chr12:50101359-50101409	HRCEpiC	kidney:	n/a
46	chr12:50101359-50101409	GM12878	blood:	n/a
47	chr12:50101363-50101413	GM06990	blood:	n/a
48	chr12:50101363-50101413	NH-A	brain:	n/a
49	chr12:50101363-50101413	HEK293	kidney:	embryo
50	chr12:50101359-50101409	HNPCEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50030390..50031784-chr12:50101029..50101967,6	MCF-7	breast:
2	chr12:50097894..50103527-chr12:50133840..50136991,8	K562	blood:
3	chr12:50097260..50102816-chr12:50134110..50137683,7	MCF-7	breast:
4	chr12:50035942..50038224-chr12:50100136..50103040,3	MCF-7	breast:
5	chr12:50030609..50032918-chr12:50100785..50102656,2	K562	blood:
6	chr12:50035466..50036448-chr12:50101094..50101950,2	K562	blood:
7	chr12:50096479..50103459-chr12:50133671..50138995,13	K562	blood:
8	chr12:50030609..50033291-chr12:50101156..50102921,3	K562	blood:
9	chr12:50100220..50104044-chr12:50234202..50236972,3	K562	blood:
10	chr12:50034899..50039875-chr12:50099580..50104040,10	MCF-7	breast:
11	chr12:50099890..50103139-chr12:50133844..50137712,5	MCF-7	breast:
12	chr12:50015541..50018481-chr12:50099736..50102606,3	MCF-7	breast:
13	chr12:49715364..49717044-chr12:50101181..50102827,2	K562	blood:
14	chr12:50030686..50032288-chr12:50100112..50102042,2	MCF-7	breast:
15	chr12:50015702..50019275-chr12:50098468..50101444,3	MCF-7	breast:
16	chr12:50100712..50101488-chrX:47004245..47004840,2	Hela-S3	cervix:
17	chr12:50030397..50032032-chr12:50101308..50102118,8	K562	blood:
18	chr12:50099618..50102364-chr12:50142236..50145462,3	K562	blood:
19	chr12:50035440..50045362-chr12:50096806..50104789,13	K562	blood:
20	chr12:50033388..50039946-chr12:50098324..50104633,12	K562	blood:
21	chr12:50015348..50017930-chr12:50100590..50103903,3	K562	blood:

Variant related genes	Relation type
ENSG00000257570	TF binding region
TMBIM6	TF binding region
FMNL3	TF binding region
ENSG00000257570	CpG island
FMNL3	CpG island
TMBIM6	CpG island
ENSG00000139644	Chromatin interaction
ENSG00000147123	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000182872	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000161791	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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	esv3356835	chr12:50100110-50102658	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50098800-50101600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr12:50099000-50101600	Active TSS	Fetal Kidney	kidney
3	chr12:50099400-50101600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:50099600-50101600	Active TSS	Liver	Liver
5	chr12:50099600-50101600	Active TSS	Brain Anterior Caudate	brain
6	chr12:50099600-50101600	Active TSS	GM12878-XiMat	blood
7	chr12:50099600-50101800	Active TSS	HSMM	muscle
8	chr12:50099800-50101600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr12:50099800-50101600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:50099800-50101600	Active TSS	Adipose Nuclei	Adipose
11	chr12:50099800-50101600	Active TSS	HSMMtube	muscle
12	chr12:50100000-50101600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:50100000-50101600	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr12:50100000-50101600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:50100000-50101600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:50100000-50101600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr12:50100000-50101600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:50100000-50101600	Active TSS	Brain Cingulate Gyrus	brain
19	chr12:50100000-50101600	Active TSS	Brain Hippocampus Middle	brain
20	chr12:50100000-50101600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:50100000-50101600	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr12:50100000-50101600	Active TSS	Rectal Smooth Muscle	rectum
23	chr12:50100000-50101600	Active TSS	NHDF-Ad	bronchial
24	chr12:50100000-50101600	Active TSS	Osteobl	bone
25	chr12:50100000-50101800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr12:50100000-50101800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:50100000-50101800	Active TSS	Colon Smooth Muscle	Colon
28	chr12:50100200-50101600	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr12:50100200-50101600	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr12:50100200-50101600	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr12:50100200-50101600	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr12:50100200-50101600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:50100200-50101600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:50100200-50101600	Active TSS	Muscle Satellite Cultured Cells	--
35	chr12:50100200-50101800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:50100200-50101800	Active TSS	Brain Germinal Matrix	brain
37	chr12:50100200-50102000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:50100200-50102200	Active TSS	Brain Angular Gyrus	brain
39	chr12:50100400-50101600	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr12:50100400-50101600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:50100400-50101600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:50100400-50101600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:50100400-50101600	Active TSS	Duodenum Mucosa	Duodenum
44	chr12:50100400-50101600	Active TSS	Stomach Smooth Muscle	stomach
45	chr12:50100400-50101600	Active TSS	HMEC	breast
46	chr12:50100400-50101600	Active TSS	K562	blood
47	chr12:50100400-50102200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:50100600-50101600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:50100600-50101600	Active TSS	Primary B cells from peripheral blood	blood
50	chr12:50100600-50101600	Active TSS	Primary hematopoietic stem cells short term culture	blood

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