Variant report

Variant	rs55797709
Chromosome Location	chr5:52773719-52773720
allele	A/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	CTCF	chr5:52773380-52774821	A549	lung:	n/a	chr5:52774337-52774358 chr5:52774335-52774353 chr5:52774336-52774352
2	E2F4	chr5:52773549-52773749	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FST	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11951354	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423554	0.86[ASN][1000 genomes]
rs56286982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370475	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6880850	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv328038	chr5:52772280-52777292	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52761600-52774400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:52766800-52774400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:52768000-52774200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:52768600-52774000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:52769200-52774000	Enhancers	HepG2	liver
6	chr5:52769800-52774000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:52770000-52774000	Weak transcription	NHEK	skin
8	chr5:52770800-52774200	Enhancers	Liver	Liver
9	chr5:52772200-52774000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:52772600-52774400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:52772800-52774400	Weak transcription	Brain Germinal Matrix	brain
12	chr5:52773000-52774000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr5:52773000-52774000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr5:52773000-52774000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:52773000-52774000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:52773000-52774000	Weak transcription	Brain Anterior Caudate	brain
17	chr5:52773200-52774000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:52773200-52774000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:52773200-52774000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:52773200-52774000	Weak transcription	Hela-S3	cervix
21	chr5:52773200-52774000	Weak transcription	HSMMtube	muscle
22	chr5:52773200-52774200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:52773200-52774400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:52773200-52774400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:52773200-52774400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:52773200-52774400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:52773400-52773800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:52773400-52773800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:52773400-52773800	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:52773400-52773800	Weak transcription	HMEC	breast
31	chr5:52773400-52774400	Weak transcription	Brain Substantia Nigra	brain
32	chr5:52773400-52774400	Weak transcription	HSMM	muscle

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