Variant report

Variant	rs142662129
Chromosome Location	chr12:50595619-50595620
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	GATA3	chr12:50595608-50596475	T-47D	breast:	n/a	n/a
2	FOXM1	chr12:50595592-50596701	ECC-1	luminal epithelium:	n/a	n/a
3	JUND	chr12:50595600-50596522	T-47D	breast:	n/a	chr12:50596207-50596217 chr12:50595857-50595867 chr12:50595857-50595867 chr12:50595857-50595867 chr12:50595857-50595867
4	GATA3	chr12:50595370-50596724	MCF-7	breast:	n/a	n/a
5	EP300	chr12:50595602-50596530	T-47D	breast:	n/a	chr12:50596271-50596280
6	TCF12	chr12:50595606-50596461	SK-N-SH	brain:	n/a	n/a
7	SRF	chr12:50595593-50596608	HCT-116	colon:	n/a	n/a
8	EP300	chr12:50595618-50596482	SK-N-SH	brain:	n/a	chr12:50596271-50596280
9	FOSL1	chr12:50595605-50596544	HCT-116	colon:	n/a	chr12:50596207-50596217 chr12:50595857-50595867 chr12:50595857-50595867 chr12:50595857-50595867 chr12:50595857-50595867
10	TEAD4	chr12:50595609-50596520	ECC-1	luminal epithelium:	n/a	chr12:50595841-50595850
11	GATA3	chr12:50595617-50596410	T-47D	breast:	n/a	n/a
12	CBX3	chr12:50595606-50596493	HCT-116	colon:	n/a	n/a
13	NR2F2	chr12:50595513-50596489	MCF-7	breast:	n/a	n/a
14	TCF12	chr12:50595524-50596460	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr12:50595538-50596205	HUVEC	blood vessel:	n/a	n/a
16	TEAD4	chr12:50595606-50596377	SK-N-SH	brain:	n/a	chr12:50595841-50595850
17	CEBPB	chr12:50595618-50596590	HCT-116	colon:	n/a	n/a
18	EP300	chr12:50595548-50596347	SK-N-SH	brain:	n/a	chr12:50596271-50596280
19	STAT3	chr12:50595592-50596406	MCF10A-Er-Src	breast:	n/a	n/a
20	ESR1	chr12:50595609-50596342	T-47D	breast:	n/a	n/a
21	RXRA	chr12:50595598-50596310	SK-N-SH	brain:	n/a	chr12:50595779-50595788
22	SIN3AK20	chr12:50595525-50596471	MCF-7	breast:	n/a	n/a
23	SIN3AK20	chr12:50595586-50596556	MCF-7	breast:	n/a	n/a
24	GATA3	chr12:50595601-50596455	SK-N-SH	brain:	n/a	n/a
25	STAT3	chr12:50595577-50596384	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50594550..50596135-chr12:50613800..50616360,2	K562	blood:
2	chr12:50477720..50479464-chr12:50594213..50596665,2	MCF-7	breast:

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000050405	Chromatin interaction
ENSG00000066117	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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:50571800-50595800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:50571800-50597000	Weak transcription	Thymus	Thymus
6	chr12:50571800-50597600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
9	chr12:50579600-50598000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:50580400-50595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:50581800-50601000	Weak transcription	Brain Substantia Nigra	brain
12	chr12:50582000-50596000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:50582400-50596200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:50582400-50598200	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:50582400-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:50582600-50597000	Weak transcription	Fetal Brain Female	brain
17	chr12:50582600-50598000	Weak transcription	Psoas Muscle	Psoas
18	chr12:50582600-50598200	Weak transcription	Pancreas	Pancrea
19	chr12:50582800-50614000	Weak transcription	Brain Angular Gyrus	brain
20	chr12:50582800-50614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:50583000-50614400	Weak transcription	Brain Anterior Caudate	brain
22	chr12:50583400-50598200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr12:50583400-50600800	Strong transcription	Adipose Nuclei	Adipose
24	chr12:50584600-50595800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:50584600-50596400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:50586000-50599600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:50586800-50595800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:50586800-50596000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:50587000-50597600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:50587800-50599800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:50588000-50599800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:50588400-50599600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:50588400-50600200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:50588400-50600600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:50588400-50600600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:50589000-50595800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:50589400-50599800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:50589400-50599800	Strong transcription	GM12878-XiMat	blood
41	chr12:50589400-50600800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:50589600-50598400	Genic enhancers	Osteobl	bone
43	chr12:50590600-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:50590600-50600200	Strong transcription	Fetal Thymus	thymus
45	chr12:50590800-50599800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:50590800-50600000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:50591000-50598000	Weak transcription	Brain Germinal Matrix	brain
48	chr12:50591000-50600200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:50591000-50603000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr12:50591600-50597600	Weak transcription	Colonic Mucosa	Colon

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