Variant report

Variant	rs4705550
Chromosome Location	chr5:112573693-112573694
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	EP300	chr5:112573689-112573953	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr5:112572466-112576241	SK-N-SH	brain:	n/a	chr5:112572962-112572976
3	GATA3	chr5:112573334-112573986	SH-SY5Y	brain:	n/a	chr5:112573963-112573973
4	MXI1	chr5:112573008-112574714	SK-N-SH	brain:	n/a	n/a
5	EP300	chr5:112573590-112573994	SK-N-SH_RA	brain:	n/a	n/a
6	YY1	chr5:112573678-112573898	SK-N-SH_RA	brain:	n/a	n/a
7	GATA2	chr5:112573295-112573973	SH-SY5Y	brain:	n/a	chr5:112573963-112573973

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112563565..112565158-chr5:112572143..112575087,2	MCF-7	breast:

Variant related genes	Relation type
MCC	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17135457	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2416309	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7717906	0.88[EUR][1000 genomes];0.93[ASN][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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4705550	APC	cis	frontal cortex	BrainEAC
rs4705550	YTHDC2	cis	frontal cortex	BrainEAC

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112548400-112581800	Weak transcription	Fetal Kidney	kidney
2	chr5:112557200-112585800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:112561600-112575000	Weak transcription	Right Ventricle	heart
4	chr5:112566400-112574000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:112568600-112575000	Weak transcription	Left Ventricle	heart
6	chr5:112568800-112575200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:112569000-112575400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:112569000-112577800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:112569600-112574000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr5:112569600-112575400	Weak transcription	Fetal Brain Female	brain
11	chr5:112570000-112574000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:112570200-112574000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:112570200-112576200	Enhancers	Fetal Heart	heart
14	chr5:112570800-112580600	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:112571000-112581400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:112571400-112574800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:112571600-112574200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:112571800-112579400	Weak transcription	Esophagus	oesophagus
19	chr5:112572000-112581400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:112572200-112576200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:112572400-112574000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr5:112572400-112574800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:112572400-112575400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr5:112572400-112580800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:112572400-112590400	Weak transcription	Liver	Liver
26	chr5:112572600-112574600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:112572600-112577200	Weak transcription	HMEC	breast
28	chr5:112572600-112585800	Weak transcription	Pancreas	Pancrea
29	chr5:112572800-112573800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:112572800-112574000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:112572800-112574000	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr5:112572800-112575400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr5:112572800-112578200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:112572800-112581800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr5:112573200-112574000	Enhancers	Fetal Brain Male	brain
36	chr5:112573200-112574000	Enhancers	Right Atrium	heart
37	chr5:112573200-112574000	Enhancers	NHEK	skin
38	chr5:112573200-112574600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:112573400-112574000	Enhancers	H9 Cell Line	embryonic stem cell
40	chr5:112573400-112574000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:112573400-112574000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:112573400-112575400	Enhancers	Colon Smooth Muscle	Colon
43	chr5:112573400-112579400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:112573600-112574000	Enhancers	Ovary	ovary
45	chr5:112573600-112574200	Enhancers	Fetal Lung	lung
46	chr5:112573600-112575000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:112573600-112575000	Enhancers	Adipose Nuclei	Adipose
48	chr5:112573600-112575600	Enhancers	Fetal Stomach	stomach
49	chr5:112573600-112577400	Weak transcription	Psoas Muscle	Psoas

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