Variant report

Variant	rs62370480
Chromosome Location	chr5:52774510-52774511
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	RAD21	chr5:52774098-52774556	HepG2	liver:	n/a	chr5:52774336-52774355
2	RAD21	chr5:52774055-52774643	H1-hESC	embryonic stem cell:	n/a	chr5:52774336-52774355
3	CHD1	chr5:52773963-52779659	IMR90	lung:	n/a	chr5:52776596-52776606 chr5:52777700-52777710 chr5:52776601-52776611
4	RAD21	chr5:52773988-52774616	A549	lung:	n/a	chr5:52774336-52774355
5	PBX3	chr5:52774113-52775064	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr5:52774125-52774524	SK-N-SH_RA	brain:	n/a	chr5:52774337-52774358 chr5:52774335-52774353 chr5:52774336-52774352
7	POLR2A	chr5:52774254-52775012	HepG2	liver:	n/a	n/a
8	RAD21	chr5:52774108-52774607	ECC-1	luminal epithelium:	n/a	chr5:52774336-52774355
9	SMC3	chr5:52774159-52774533	K562	blood:	n/a	chr5:52774337-52774351
10	SMC3	chr5:52774129-52774608	Hela-S3	cervix:	n/a	chr5:52774337-52774351
11	POLR2A	chr5:52774125-52774957	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr5:52774386-52777094	HepG2	liver:	n/a	n/a
13	POLR2A	chr5:52774291-52774872	Hela-S3	cervix:	n/a	n/a
14	MAZ	chr5:52774221-52774557	GM12878	blood:	n/a	n/a
15	RAD21	chr5:52774017-52774651	HCT-116	colon:	n/a	chr5:52774336-52774355
16	TCF7L2	chr5:52774131-52774955	HCT-116	colon:	n/a	chr5:52774792-52774799
17	CTBP2	chr5:52774216-52774926	H1-hESC	embryonic stem cell:	n/a	n/a
18	GATA3	chr5:52774106-52777467	SK-N-SH	brain:	n/a	chr5:52774928-52774936 chr5:52776733-52776741
19	CTCF	chr5:52774480-52774630	GM12864	blood:	n/a	n/a
20	JUND	chr5:52774224-52774947	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr5:52774480-52774630	GM12868	blood:	n/a	n/a
22	TBP	chr5:52774269-52774889	HepG2	liver:	n/a	n/a
23	RAD21	chr5:52774151-52774853	HepG2	liver:	n/a	chr5:52774336-52774355
24	RCOR1	chr5:52774247-52774847	HepG2	liver:	n/a	n/a
25	CTCF	chr5:52774360-52774510	HCM	heart:	n/a	n/a
26	NFIC	chr5:52774272-52774677	HepG2	liver:	n/a	n/a
27	CTCF	chr5:52774096-52774542	GM12878	blood:	n/a	chr5:52774337-52774358 chr5:52774335-52774353 chr5:52774336-52774352
28	TCF7L2	chr5:52774089-52774788	PANC-1	pancreas:	n/a	n/a
29	SP4	chr5:52774160-52774557	H1-hESC	embryonic stem cell:	n/a	n/a
30	SIN3A	chr5:52774199-52774968	H1-hESC	embryonic stem cell:	n/a	n/a
31	TCF12	chr5:52774227-52775011	A549	lung:	n/a	chr5:52774753-52774760
32	RAD21	chr5:52774058-52774691	HCT-116	colon:	n/a	chr5:52774336-52774355
33	CHD1	chr5:52774236-52774872	H1-hESC	embryonic stem cell:	n/a	n/a
34	MBD4	chr5:52774075-52775671	HepG2	liver:	n/a	n/a
35	GTF2F1	chr5:52774299-52774727	H1-hESC	embryonic stem cell:	n/a	n/a
36	RAD21	chr5:52774129-52774538	GM12878	blood:	n/a	chr5:52774336-52774355
37	MYC	chr5:52774186-52774861	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr5:52774114-52774625	MCF-7	breast:	n/a	chr5:52774336-52774355
39	HEY1	chr5:52774155-52777346	HepG2	liver:	n/a	chr5:52776435-52776450 chr5:52776602-52776617 chr5:52774757-52774772
40	POLR2A	chr5:52774375-52780496	HepG2	liver:	n/a	n/a
41	CTCF	chr5:52774106-52774541	K562	blood:	n/a	chr5:52774337-52774358 chr5:52774335-52774353 chr5:52774336-52774352
42	RAD21	chr5:52774123-52774763	IMR90	lung:	n/a	chr5:52774336-52774355
43	RAD21	chr5:52774161-52774685	H1-hESC	embryonic stem cell:	n/a	chr5:52774336-52774355
44	ZNF143	chr5:52774168-52774548	GM12878	blood:	n/a	n/a
45	CTCF	chr5:52773881-52774625	HCT-116	colon:	n/a	chr5:52774337-52774358 chr5:52774335-52774353 chr5:52774336-52774352
46	CTCF	chr5:52774062-52774531	A549	lung:	n/a	chr5:52774337-52774358 chr5:52774335-52774353 chr5:52774336-52774352
47	TCF7L2	chr5:52774184-52774882	Hela-S3	cervix:	n/a	chr5:52774792-52774799
48	POLR2A	chr5:52774274-52774988	HepG2	liver:	n/a	n/a
49	MAX	chr5:52774168-52774856	SK-N-SH	brain:	n/a	n/a
50	CTCF	chr5:52774195-52774510	H1-hESC	embryonic stem cell:	n/a	chr5:52774337-52774358 chr5:52774335-52774353 chr5:52774336-52774352

No.	Distal block	Cell Line	Cell type
1	chr5:52774220..52774824-chr5:53287438..53288055,2	MCF-7	breast:
2	chr5:52773843..52774731-chr5:53166346..53167079,2	MCF-7	breast:
3	chr5:52774231..52774841-chr5:52855913..52856842,2	MCF-7	breast:
4	chr5:52773878..52774764-chr5:53524810..53525607,3	MCF-7	breast:
5	chr5:52774000..52774674-chr5:53166806..53167591,2	MCF-7	breast:
6	chr5:52774119..52774818-chr5:53166203..53166706,2	K562	blood:

Variant related genes	Relation type
FST	TF binding region
ENSG00000164258	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs55744247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55873647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62370471	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62370472	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62370473	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62370474	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62370476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52774000-52774600	Bivalent Enhancer	Fetal Intestine Large	intestine
2	chr5:52774000-52774600	Flanking Active TSS	HepG2	liver
3	chr5:52774200-52774600	Flanking Active TSS	Brain Cingulate Gyrus	brain
4	chr5:52774200-52774600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr5:52774200-52774600	Active TSS	Fetal Muscle Trunk	muscle
6	chr5:52774200-52774600	Flanking Active TSS	NHLF	lung
7	chr5:52774200-52774800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
8	chr5:52774200-52774800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
9	chr5:52774200-52775200	Bivalent/Poised TSS	GM12878-XiMat	blood
10	chr5:52774200-52775400	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:52774200-52775400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr5:52774200-52775600	Flanking Active TSS	Liver	Liver
13	chr5:52774200-52775800	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr5:52774200-52776600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr5:52774200-52776600	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr5:52774200-52776600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr5:52774200-52776600	Active TSS	Ovary	ovary
18	chr5:52774200-52776600	Active TSS	Stomach Smooth Muscle	stomach
19	chr5:52774200-52776800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr5:52774200-52776800	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr5:52774200-52776800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:52774200-52777200	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr5:52774200-52777400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:52774200-52778200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:52774200-52778800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:52774200-52778800	Active TSS	Osteobl	bone
27	chr5:52774200-52779000	Active TSS	Colon Smooth Muscle	Colon
28	chr5:52774200-52779200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr5:52774400-52774600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:52774400-52774600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
31	chr5:52774400-52774600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
32	chr5:52774400-52774600	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr5:52774400-52774600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:52774400-52774600	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:52774400-52774600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:52774400-52774600	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
37	chr5:52774400-52774600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:52774400-52774600	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr5:52774400-52774600	Active TSS	Brain Hippocampus Middle	brain
40	chr5:52774400-52774600	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr5:52774400-52774600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
42	chr5:52774400-52774600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
43	chr5:52774400-52774600	Active TSS	Fetal Stomach	stomach
44	chr5:52774400-52774600	Flanking Active TSS	Left Ventricle	heart
45	chr5:52774400-52774600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
46	chr5:52774400-52774600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
47	chr5:52774400-52774600	Flanking Active TSS	Right Atrium	heart
48	chr5:52774400-52774600	Flanking Active TSS	NHEK	skin
49	chr5:52774400-52774800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
50	chr5:52774400-52774800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood

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