Variant report

Variant	rs4140696
Chromosome Location	chr12:45445256-45445257
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	FOXP2	chr12:45445046-45445302	SK-N-MC	brain:	n/a	n/a
2	ZBTB7A	chr12:45444591-45445542	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr12:45444498-45445463	ECC-1	luminal epithelium:	n/a	chr12:45444931-45444941
4	TCF12	chr12:45444517-45445469	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr12:45445050-45445359	ECC-1	luminal epithelium:	n/a	n/a
6	ZNF263	chr12:45444635-45445264	HEK293-T-REx	kidney:	n/a	chr12:45445164-45445173
7	TCF12	chr12:45444584-45445439	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr12:45444467-45445341	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr12:45445101-45445300	MCF-7	breast:	n/a	n/a
10	CTBP2	chr12:45443795-45445560	H1-hESC	embryonic stem cell:	n/a	n/a
11	BACH1	chr12:45445037-45445376	H1-hESC	embryonic stem cell:	n/a	n/a
12	ZBTB7A	chr12:45444733-45445541	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr12:45444574-45445323	ECC-1	luminal epithelium:	n/a	n/a
14	MYC	chr12:45445112-45445281	MCF-7	breast:	n/a	n/a
15	SIN3A	chr12:45443931-45445486	H1-hESC	embryonic stem cell:	n/a	chr12:45444855-45444868 chr12:45444724-45444735 chr12:45444769-45444782
16	POLR2A	chr12:45445049-45445282	A549	lung:	n/a	n/a

Variant related genes	Relation type
DBX2	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11182810	0.88[EUR][1000 genomes]
rs11182811	0.88[EUR][1000 genomes]
rs1495033	0.86[EUR][1000 genomes]
rs1495034	0.84[EUR][1000 genomes]
rs1495042	0.88[EUR][1000 genomes]
rs1921551	0.94[ASN][1000 genomes]
rs2544102	0.86[EUR][1000 genomes]
rs2643140	0.86[EUR][1000 genomes]
rs268046	0.86[ASN][1000 genomes]
rs2731034	0.94[ASN][1000 genomes]
rs2731040	0.84[EUR][1000 genomes]
rs2731053	0.86[EUR][1000 genomes]
rs2731054	0.86[EUR][1000 genomes]
rs4561266	0.84[EUR][1000 genomes]

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	esv3351644	chr12:45345597-45529449	Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1045857	chr12:45351172-45468784	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv541485	chr12:45351172-45468784	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4140696	RP11-478B9.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4140696	DBX2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45441400-45445400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:45443000-45445600	Active TSS	Right Atrium	heart
3	chr12:45443400-45445600	Active TSS	Brain Anterior Caudate	brain
4	chr12:45443400-45445600	Active TSS	Brain Cingulate Gyrus	brain
5	chr12:45443400-45445800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr12:45443400-45446000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:45443600-45445600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:45443600-45445800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:45443800-45445400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:45443800-45445600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:45443800-45445600	Bivalent Enhancer	Liver	Liver
12	chr12:45443800-45445800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:45444000-45445400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:45444000-45445600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:45444000-45445800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr12:45444000-45445800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
17	chr12:45444000-45445800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr12:45444000-45445800	Active TSS	Brain Angular Gyrus	brain
19	chr12:45444200-45445400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr12:45444200-45445400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr12:45444200-45445400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:45444200-45445400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:45444200-45445400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:45444200-45445600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:45444200-45445600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:45444200-45445600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:45444200-45445600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:45444200-45445600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
29	chr12:45444200-45445600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:45444200-45445600	Active TSS	Rectal Smooth Muscle	rectum
31	chr12:45444200-45445800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
32	chr12:45444200-45445800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:45444200-45446000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:45444400-45445400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:45444400-45445400	Bivalent/Poised TSS	Esophagus	oesophagus
36	chr12:45444400-45445400	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr12:45444400-45445400	Bivalent/Poised TSS	Left Ventricle	heart
38	chr12:45444400-45445600	Flanking Bivalent TSS/Enh	HMEC	breast
39	chr12:45444600-45445400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:45444600-45445400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:45444600-45445400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr12:45444600-45445400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
43	chr12:45444600-45445400	Bivalent/Poised TSS	Thymus	Thymus
44	chr12:45444600-45445400	Bivalent/Poised TSS	HSMM	muscle
45	chr12:45444600-45445400	Bivalent/Poised TSS	NHEK	skin
46	chr12:45444600-45445600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:45444600-45445600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
48	chr12:45444600-45445600	Bivalent/Poised TSS	HepG2	liver
49	chr12:45444600-45445800	Bivalent/Poised TSS	NH-A	brain
50	chr12:45444800-45445400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon

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