Variant report

Variant	rs72554691
Chromosome Location	chr5:42808371-42808372
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:57)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:57 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr5:42808177-42808564	HepG2	liver:	n/a	n/a
2	CTCF	chr5:42808325-42808505	Kidney_OC	kidney:	n/a	n/a
3	SMC3	chr5:42808203-42808704	HepG2	liver:	n/a	n/a
4	CTCF	chr5:42808320-42808470	Caco-2	colon:	n/a	n/a
5	EP300	chr5:42808217-42808591	HepG2	liver:	n/a	n/a
6	CTCF	chr5:42808280-42808430	MCF-7	breast:	n/a	n/a
7	RAD21	chr5:42808137-42808707	HepG2	liver:	n/a	n/a
8	RAD21	chr5:42808227-42808544	MCF-7	breast:	n/a	n/a
9	HEY1	chr5:42805975-42809968	HepG2	liver:	n/a	n/a
10	HEY1	chr5:42808130-42808717	HepG2	liver:	n/a	n/a
11	CTCF	chr5:42808295-42808518	MCF-7	breast:	n/a	n/a
12	CTCF	chr5:42808320-42808470	HepG2	liver:	n/a	n/a
13	RAD21	chr5:42808247-42808634	HepG2	liver:	n/a	n/a
14	MYBL2	chr5:42808031-42808714	HepG2	liver:	n/a	n/a
15	FOXA1	chr5:42808191-42808517	HepG2	liver:	n/a	n/a
16	NFIC	chr5:42807733-42808685	HepG2	liver:	n/a	n/a
17	CTCF	chr5:42808339-42808473	MCF-7	breast:	n/a	n/a
18	MYBL2	chr5:42807377-42809776	HepG2	liver:	n/a	n/a
19	CTCF	chr5:42808340-42808490	HMEC	breast:	n/a	n/a
20	MBD4	chr5:42807663-42808493	HepG2	liver:	n/a	n/a
21	CTCF	chr5:42808338-42808469	K562	blood:	n/a	n/a
22	RAD21	chr5:42808188-42808606	HepG2	liver:	n/a	n/a
23	TBL1XR1	chr5:42808354-42808482	K562	blood:	n/a	n/a
24	CTCF	chr5:42808272-42808537	HepG2	liver:	n/a	n/a
25	CTCF	chr5:42808300-42808450	NHEK	skin:	n/a	n/a
26	HDAC2	chr5:42808181-42808475	HepG2	liver:	n/a	n/a
27	CTCF	chr5:42808320-42808470	RPTEC	kidney:	n/a	n/a
28	CTCF	chr5:42808338-42808452	MCF-7	breast:	n/a	n/a
29	REST	chr5:42808138-42808827	HepG2	liver:	n/a	n/a
30	MAZ	chr5:42807916-42808483	HepG2	liver:	n/a	n/a
31	RAD21	chr5:42808189-42808516	H1-hESC	embryonic stem cell:	n/a	n/a
32	TEAD4	chr5:42807953-42808686	HepG2	liver:	n/a	n/a
33	CTCF	chr5:42808279-42808574	K562	blood:	n/a	n/a
34	CTCF	chr5:42808260-42808410	HMF	breast:	n/a	n/a
35	CTCF	chr5:42808340-42808490	HepG2	liver:	n/a	n/a
36	CTCF	chr5:42808360-42808510	HEK293	kidney:	n/a	n/a
37	SMC3	chr5:42808314-42808451	K562	blood:	n/a	n/a
38	FOXA2	chr5:42808150-42808474	HepG2	liver:	n/a	n/a
39	POLR2A	chr5:42805758-42812555	HepG2	liver:	n/a	n/a
40	FOXA1	chr5:42808207-42808517	T-47D	breast:	n/a	n/a
41	MBD4	chr5:42804512-42808794	HepG2	liver:	n/a	n/a
42	POLR2A	chr5:42808142-42808776	HepG2	liver:	n/a	n/a
43	POLR2A	chr5:42807619-42808796	HepG2	liver:	n/a	n/a
44	POLR2A	chr5:42808118-42809598	HepG2	liver:	n/a	n/a
45	FOXA1	chr5:42808125-42808511	T-47D	breast:	n/a	n/a
46	CTCF	chr5:42808360-42808510	K562	blood:	n/a	n/a
47	POLR2A	chr5:42797012-42808716	HepG2	liver:	n/a	n/a
48	POLR2A	chr5:42798272-42812268	HepG2	liver:	n/a	n/a
49	CTCF	chr5:42808195-42808592	HepG2	liver:	n/a	n/a
50	CTCF	chr5:42808340-42808490	HMF	breast:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42808126..42809697-chr5:42810037..42813024,2	K562	blood:

No data

Variant related genes	Relation type
SEPP1	TF binding region
ENSG00000250722	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs28919897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28919907	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28919909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28919918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34190075	1.00[AMR][1000 genomes]
rs34514470	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34516185	1.00[AMR][1000 genomes]
rs34899335	1.00[AMR][1000 genomes]
rs34980021	1.00[AMR][1000 genomes]
rs36201176	1.00[AFR][1000 genomes]
rs3877900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4132107	1.00[AMR][1000 genomes]
rs4296811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4346811	1.00[AMR][1000 genomes]
rs4591756	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6865685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6871142	1.00[AMR][1000 genomes]
rs6879044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6882361	1.00[AMR][1000 genomes]
rs7714754	1.00[AMR][1000 genomes]
rs7716660	0.94[AFR][1000 genomes]
rs7726356	1.00[AMR][1000 genomes]
rs7727354	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
9	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
10	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
14	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
15	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42789600-42813400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:42791400-42811200	Weak transcription	Fetal Thymus	thymus
3	chr5:42795600-42810200	Weak transcription	Thymus	Thymus
4	chr5:42797000-42810600	Weak transcription	Esophagus	oesophagus
5	chr5:42797400-42810800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:42797800-42809200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:42798200-42808400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:42798200-42811200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:42799000-42811600	Weak transcription	HSMMtube	muscle
10	chr5:42799600-42811400	Weak transcription	Fetal Brain Female	brain
11	chr5:42799600-42812000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:42799800-42808400	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:42800000-42809400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:42800600-42811200	Weak transcription	Small Intestine	intestine
15	chr5:42802000-42809000	Weak transcription	Right Ventricle	heart
16	chr5:42802000-42809600	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:42802000-42810200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:42802000-42810200	Weak transcription	Brain Germinal Matrix	brain
19	chr5:42802000-42810600	Weak transcription	Aorta	Aorta
20	chr5:42802000-42810600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:42802000-42810600	Weak transcription	Gastric	stomach
22	chr5:42802000-42810600	Weak transcription	Lung	lung
23	chr5:42802000-42811000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:42802000-42811200	Weak transcription	Spleen	Spleen
25	chr5:42802200-42810200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:42802400-42810600	Weak transcription	Pancreas	Pancrea
27	chr5:42802400-42810800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:42803800-42810800	Weak transcription	Fetal Brain Male	brain
29	chr5:42804600-42809400	Weak transcription	Fetal Stomach	stomach
30	chr5:42804800-42811200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:42806800-42809200	Weak transcription	Fetal Kidney	kidney
32	chr5:42807000-42809000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:42807200-42810200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:42807200-42810200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:42807200-42810800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr5:42807400-42808400	Enhancers	Brain Anterior Caudate	brain
37	chr5:42807600-42808400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:42807600-42808400	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
39	chr5:42807600-42808400	Enhancers	NHDF-Ad	bronchial
40	chr5:42807600-42808600	Transcr. at gene 5' and 3'	Liver	Liver
41	chr5:42807600-42808600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
42	chr5:42807600-42809600	Transcr. at gene 5' and 3'	HepG2	liver
43	chr5:42807600-42812600	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr5:42807800-42808400	Enhancers	Osteobl	bone
45	chr5:42807800-42808600	Transcr. at gene 5' and 3'	Fetal Lung	lung
46	chr5:42807800-42809800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:42807800-42812800	Active TSS	Right Atrium	heart
48	chr5:42808000-42808400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:42808000-42808400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:42808000-42808400	Enhancers	Muscle Satellite Cultured Cells	--

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