Variant report

Variant	rs55986721
Chromosome Location	chr5:179267506-179267507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179262507-179269414	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr5:179266135-179269441	U87	brain:	n/a	n/a
3	POLR2A	chr5:179262501-179268119	K562	blood:	n/a	n/a
4	POLR2A	chr5:179267169-179268068	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr5:179267157-179268157	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:179267221-179268273	A549	lung:	n/a	n/a
7	POLR2A	chr5:179267289-179269268	HepG2	liver:	n/a	n/a
8	POLR2A	chr5:179267276-179269236	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:179263086-179269260	IMR90	lung:	n/a	n/a
10	POLR2A	chr5:179267247-179268961	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr5:179267133-179267770	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr5:179263338-179269338	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr5:179262516-179269530	A549	lung:	n/a	n/a
14	POLR2A	chr5:179267224-179268109	A549	lung:	n/a	n/a
15	POLR2A	chr5:179267141-179268131	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr5:179267471-179268368	K562	blood:	n/a	n/a
17	POLR2A	chr5:179266049-179269325	U87	brain:	n/a	n/a
18	POLR2A	chr5:179267234-179267599	HCT-116	colon:	n/a	n/a
19	POLR2A	chr5:179267407-179267696	SK-N-SH	brain:	n/a	n/a
20	ZNF263	chr5:179267396-179268163	HEK293-T-REx	kidney:	n/a	n/a
21	TCF12	chr5:179267076-179267631	A549	lung:	n/a	n/a
22	POLR2A	chr5:179267488-179267819	HepG2	liver:	n/a	n/a
23	POLR2A	chr5:179262939-179269368	U87	brain:	n/a	n/a
24	POLR2A	chr5:179267383-179268091	HepG2	liver:	n/a	n/a
25	BCL3	chr5:179267094-179269114	A549	lung:	n/a	n/a
26	POLR2A	chr5:179262545-179268187	HepG2	liver:	n/a	n/a
27	POLR2A	chr5:179267215-179267659	HUVEC	blood vessel:	n/a	n/a
28	JUND	chr5:179267236-179268257	A549	lung:	n/a	n/a
29	POLR2A	chr5:179267400-179268044	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr5:179267413-179267809	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr5:179267408-179268231	A549	lung:	n/a	n/a
32	POLR2A	chr5:179267500-179268110	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:179267341-179267795	GM12891	blood:	n/a	n/a
34	POLR2A	chr5:179267231-179268160	MCF-7	breast:	n/a	n/a
35	ELF1	chr5:179267278-179268195	A549	lung:	n/a	n/a
36	PBX3	chr5:179267195-179268236	A549	lung:	n/a	n/a
37	POLR2A	chr5:179267300-179268021	GM12878	blood:	n/a	n/a
38	POLR2A	chr5:179267334-179268064	GM12878	blood:	n/a	n/a
39	BCL3	chr5:179266098-179268744	A549	lung:	n/a	n/a
40	POLR2A	chr5:179267420-179267658	A549	lung:	n/a	n/a
41	POLR2A	chr5:179267134-179267758	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr5:179262984-179269243	U87	brain:	n/a	n/a
43	POLR2A	chr5:179262643-179268223	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr5:179267354-179267912	HepG2	liver:	n/a	n/a
45	POLR2A	chr5:179267427-179268236	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179204097..179205986-chr5:179266401..179268653,2	K562	blood:
2	chr5:179246564..179250154-chr5:179266751..179272341,6	MCF-7	breast:
3	chr5:179193680..179196037-chr5:179266689..179269307,2	K562	blood:

No data

Variant related genes	Relation type
C5orf45	TF binding region
ENSG00000161011	Chromatin interaction
ENSG00000161021	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs55782074	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56225166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57713691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58652165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58713160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60403632	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60462250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61613267	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61748794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73334031	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73334055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73334063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335948	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73351618	1.00[AMR][1000 genomes]
rs73810204	1.00[AMR][1000 genomes]
rs73810488	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
7	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
8	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
9	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
10	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
11	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179250200-179272000	Strong transcription	Fetal Muscle Leg	muscle
2	chr5:179250200-179272800	Weak transcription	Fetal Brain Male	brain
3	chr5:179251800-179267800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr5:179255000-179268800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:179255200-179269000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:179258200-179274800	Weak transcription	Fetal Heart	heart
7	chr5:179262400-179268600	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr5:179262400-179269000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:179262400-179269200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:179262400-179269400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:179262400-179269400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:179262400-179269400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:179262400-179269400	Strong transcription	Brain Angular Gyrus	brain
14	chr5:179262400-179271000	Strong transcription	Fetal Stomach	stomach
15	chr5:179262400-179271400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:179262400-179271600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:179262400-179272000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:179262600-179269000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:179262600-179269000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:179262600-179269200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:179262600-179279400	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr5:179262800-179269200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr5:179263000-179268200	Strong transcription	Primary B cells from cord blood	blood
24	chr5:179263000-179269000	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr5:179263000-179269200	Strong transcription	Primary T cells from cord blood	blood
26	chr5:179263000-179269800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:179263000-179271000	Strong transcription	Brain Germinal Matrix	brain
28	chr5:179263000-179271400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:179263000-179271800	Strong transcription	Fetal Lung	lung
30	chr5:179263000-179279600	Strong transcription	Brain Anterior Caudate	brain
31	chr5:179263000-179279800	Strong transcription	Brain Hippocampus Middle	brain
32	chr5:179263000-179280400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:179263200-179268200	Strong transcription	Thymus	Thymus
34	chr5:179263200-179269000	Strong transcription	Brain Substantia Nigra	brain
35	chr5:179263200-179269600	Strong transcription	Fetal Brain Female	brain
36	chr5:179263600-179267800	Strong transcription	Adipose Nuclei	Adipose
37	chr5:179263600-179280200	Strong transcription	Colon Smooth Muscle	Colon
38	chr5:179263800-179268200	Strong transcription	NHLF	lung
39	chr5:179263800-179269000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:179263800-179269000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr5:179263800-179269000	Strong transcription	Rectal Smooth Muscle	rectum
42	chr5:179263800-179269200	Strong transcription	Placenta	Placenta
43	chr5:179263800-179271000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:179263800-179271800	Strong transcription	Ovary	ovary
45	chr5:179264000-179269000	Strong transcription	Colonic Mucosa	Colon
46	chr5:179264000-179269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:179264000-179269400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:179264000-179269400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:179264000-179269600	Strong transcription	Esophagus	oesophagus
50	chr5:179264000-179271200	Strong transcription	Stomach Smooth Muscle	stomach

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