Variant report

Variant	rs558611524
Chromosome Location	chr12:50097691-50097692
allele	A/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	STAT1	chr12:50097188-50097776	GM12878	blood:	n/a	chr12:50097241-50097253 chr12:50097486-50097500
2	EP300	chr12:50097598-50097744	GM12878	blood:	n/a	n/a
3	GATA3	chr12:50097381-50098078	SK-N-SH	brain:	n/a	chr12:50097741-50097748
4	MAFK	chr12:50097438-50097846	IMR90	lung:	n/a	chr12:50097598-50097608 chr12:50097599-50097608
5	YY1	chr12:50097476-50097823	GM12892	blood:	n/a	n/a
6	YY1	chr12:50097519-50097847	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:50096637-50097881	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:50096226-50101443	GM12878	blood:	n/a	n/a
9	NFATC1	chr12:50096551-50097867	GM12878	blood:	n/a	n/a
10	SPI1	chr12:50097416-50097772	GM12878	blood:	n/a	n/a
11	RELA	chr12:50097166-50098114	GM12878	blood:	n/a	chr12:50097643-50097652 chr12:50097643-50097652
12	POLR2A	chr12:50096453-50098183	GM12878	blood:	n/a	n/a
13	RUNX3	chr12:50097130-50098205	GM12878	blood:	n/a	n/a
14	CHD2	chr12:50097132-50097691	GM12878	blood:	n/a	n/a
15	MXI1	chr12:50097380-50098033	GM12878	blood:	n/a	n/a
16	YY1	chr12:50097450-50097858	GM12891	blood:	n/a	n/a
17	STAT3	chr12:50097285-50098174	GM12878	blood:	n/a	chr12:50097486-50097500
18	POLR2A	chr12:50096717-50097991	GM12891	blood:	n/a	n/a
19	YY1	chr12:50097432-50097871	GM12878	blood:	n/a	n/a
20	TAF1	chr12:50097454-50097808	GM12878	blood:	n/a	n/a
21	TBP	chr12:50096684-50098070	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:50096215-50098262	GM12878	blood:	n/a	n/a
23	RUNX3	chr12:50097083-50097831	GM12878	blood:	n/a	n/a
24	ATF2	chr12:50097132-50097895	GM12878	blood:	n/a	n/a
25	NFATC1	chr12:50097206-50098146	GM12878	blood:	n/a	n/a
26	TCF12	chr12:50097394-50097744	GM12878	blood:	n/a	n/a
27	YY1	chr12:50097390-50097897	GM12878	blood:	n/a	n/a
28	TCF12	chr12:50097156-50098098	SK-N-SH	brain:	n/a	n/a
29	ATF2	chr12:50096327-50097968	GM12878	blood:	n/a	n/a
30	RELA	chr12:50096518-50098048	GM12891	blood:	n/a	chr12:50097643-50097652 chr12:50097643-50097652
31	STAT5A	chr12:50096403-50097879	GM12878	blood:	n/a	chr12:50097241-50097253 chr12:50097488-50097512 chr12:50097486-50097500
32	BHLHE40	chr12:50097414-50097850	GM12878	blood:	n/a	n/a
33	SPI1	chr12:50097492-50097753	GM12891	blood:	n/a	n/a
34	SPI1	chr12:50097551-50097710	K562	blood:	n/a	n/a
35	MAZ	chr12:50097504-50097744	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:50097423-50097813	U87	brain:	n/a	n/a
37	IKZF1	chr12:50097122-50097835	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:50096279-50098500	GM12892	blood:	n/a	n/a
39	TAF1	chr12:50097394-50097802	GM12878	blood:	n/a	n/a
40	EP300	chr12:50097286-50097826	GM12878	blood:	n/a	n/a
41	RELA	chr12:50096620-50097934	GM19099	blood:	n/a	chr12:50097643-50097652 chr12:50097643-50097652
42	ZNF143	chr12:50097485-50097736	GM12878	blood:	n/a	n/a
43	BCLAF1	chr12:50097379-50097942	GM12878	blood:	n/a	n/a
44	PBX3	chr12:50097306-50097910	SK-N-SH	brain:	n/a	n/a
45	STAT5A	chr12:50097145-50097843	GM12878	blood:	n/a	chr12:50097241-50097253 chr12:50097488-50097512 chr12:50097486-50097500
46	FOS	chr12:50097622-50097762	MCF10A-Er-Src	breast:	n/a	n/a
47	EBF1	chr12:50097442-50097816	GM12878	blood:	n/a	n/a
48	TBL1XR1	chr12:50097170-50097802	GM12878	blood:	n/a	n/a
49	POLR2A	chr12:50096336-50098350	GM12892	blood:	n/a	n/a
50	EBF1	chr12:50096230-50098035	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50097260..50102816-chr12:50134110..50137683,7	MCF-7	breast:
2	chr12:50096479..50103459-chr12:50133671..50138995,13	K562	blood:
3	chr12:50090621..50092463-chr12:50096171..50099106,4	K562	blood:
4	chr12:50046987..50048509-chr12:50096714..50099634,2	MCF-7	breast:
5	chr12:50097487..50099802-chr12:50102070..50104731,2	MCF-7	breast:
6	chr12:50039220..50042213-chr12:50096453..50098982,2	MCF-7	breast:
7	chr12:50080608..50083488-chr12:50095334..50097821,2	MCF-7	breast:
8	chr12:50095907..50097744-chr12:50102018..50104730,2	K562	blood:
9	chr12:50035440..50045362-chr12:50096806..50104789,13	K562	blood:
10	chr12:50092701..50095008-chr12:50097299..50100800,3	K562	blood:
11	chr12:50067389..50069514-chr12:50096557..50099355,2	MCF-7	breast:

Variant related genes	Relation type
TMBIM6	TF binding region
ENSG00000257570	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000139644	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	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	esv3348146	chr12:50097129-50098626	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3487030	chr12:50097166-50098613	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3487019	chr12:50097200-50098558	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3487041	chr12:50097200-50098558	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv14748	chr12:50097299-50098198	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50093200-50098200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:50093200-50098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:50093200-50098800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:50093200-50099200	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:50093200-50099600	Weak transcription	Fetal Heart	heart
6	chr12:50093200-50100200	Weak transcription	Esophagus	oesophagus
7	chr12:50093400-50098600	Weak transcription	Right Ventricle	heart
8	chr12:50093400-50098800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:50093400-50099200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:50093400-50099200	Weak transcription	Colonic Mucosa	Colon
11	chr12:50093400-50099800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:50093800-50099200	Enhancers	Primary B cells from cord blood	blood
13	chr12:50094800-50099400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:50095200-50098200	Flanking Active TSS	GM12878-XiMat	blood
15	chr12:50095600-50099400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:50095800-50097800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr12:50095800-50097800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:50095800-50098000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:50095800-50098200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr12:50095800-50098800	Enhancers	Fetal Muscle Leg	muscle
21	chr12:50095800-50099000	Enhancers	Fetal Lung	lung
22	chr12:50095800-50099000	Enhancers	Left Ventricle	heart
23	chr12:50095800-50099200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:50095800-50099400	Enhancers	Fetal Thymus	thymus
25	chr12:50095800-50100000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:50096000-50099200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:50096200-50098000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:50096400-50097800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:50096400-50097800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr12:50096400-50098000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr12:50096400-50098000	Enhancers	Adipose Nuclei	Adipose
32	chr12:50096400-50098000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:50096400-50098200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:50096400-50098200	Enhancers	Brain Cingulate Gyrus	brain
35	chr12:50096400-50098800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr12:50096400-50098800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:50096400-50098800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:50096400-50099000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr12:50096400-50099000	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr12:50096400-50099000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:50096400-50099000	Enhancers	Brain Substantia Nigra	brain
42	chr12:50096400-50099000	Enhancers	Placenta	Placenta
43	chr12:50096400-50099000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr12:50096400-50099200	Enhancers	Fetal Stomach	stomach
45	chr12:50096400-50099200	Enhancers	Dnd41	blood
46	chr12:50096400-50099600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:50096400-50100000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:50096600-50098000	Enhancers	Psoas Muscle	Psoas
49	chr12:50096600-50098000	Enhancers	Thymus	Thymus
50	chr12:50096600-50098800	Weak transcription	Lung	lung

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