Variant report

Variant	rs56316727
Chromosome Location	chr5:90562179-90562180
allele	C/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	IRF1	chr5:90562172-90562517	K562	blood:	n/a	chr5:90562318-90562327 chr5:90562319-90562328
2	CTCF	chr5:90562060-90562210	HVMF	connective:	n/a	n/a
3	ATF3	chr5:90562065-90562543	K562	blood:	n/a	n/a
4	CTCF	chr5:90562120-90562270	HCPEpiC	choroid plexus:	n/a	n/a
5	JUND	chr5:90562023-90562511	Hela-S3	cervix:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493 chr5:90562317-90562328
6	FOS	chr5:90562094-90562602	MCF10A-Er-Src	breast:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562317-90562328 chr5:90562319-90562328 chr5:90562481-90562493
7	CTCF	chr5:90562160-90562310	RPTEC	kidney:	n/a	n/a
8	ATF2	chr5:90562165-90562539	GM12878	blood:	n/a	n/a
9	CTCF	chr5:90562040-90562190	GM12870	blood:	n/a	n/a
10	CTCF	chr5:90562100-90562250	HCT-116	colon:	n/a	n/a
11	CTCF	chr5:90562120-90562270	HAc	cerebellar:	n/a	n/a
12	JUND	chr5:90562159-90562519	HepG2	liver:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493 chr5:90562317-90562328
13	FOSL2	chr5:90561997-90562549	A549	lung:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493
14	JUND	chr5:90561911-90562694	HCT-116	colon:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493 chr5:90562317-90562328
15	CTCF	chr5:90562160-90562310	SAEC	small airway:	n/a	n/a
16	CTCF	chr5:90562120-90562270	AoAF	blood vessel:	n/a	n/a
17	MEF2A	chr5:90562095-90562579	K562	blood:	n/a	chr5:90562330-90562351 chr5:90562336-90562347 chr5:90562337-90562346 chr5:90562252-90562267 chr5:90562332-90562353 chr5:90562332-90562353 chr5:90562330-90562351 chr5:90562334-90562350 chr5:90562330-90562351 chr5:90562334-90562349 chr5:90562333-90562348 chr5:90562333-90562349
18	FOS	chr5:90562107-90562614	MCF10A-Er-Src	breast:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562317-90562328 chr5:90562319-90562328 chr5:90562481-90562493
19	MEF2A	chr5:90562025-90562576	GM12878	blood:	n/a	chr5:90562330-90562351 chr5:90562336-90562347 chr5:90562337-90562346 chr5:90562252-90562267 chr5:90562332-90562353 chr5:90562332-90562353 chr5:90562330-90562351 chr5:90562334-90562350 chr5:90562330-90562351 chr5:90562334-90562349 chr5:90562333-90562348 chr5:90562333-90562349
20	CTCF	chr5:90562140-90562290	NHEK	skin:	n/a	n/a
21	CTCF	chr5:90562040-90562190	GM12872	blood:	n/a	n/a
22	CTCF	chr5:90562160-90562310	HCFaa	heart:	n/a	n/a
23	CTCF	chr5:90562140-90562290	GM12872	blood:	n/a	n/a
24	JUN	chr5:90562031-90562506	K562	blood:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493
25	CTCF	chr5:90562060-90562210	HRE	kidney:	n/a	n/a
26	CUX1	chr5:90561993-90562428	K562	blood:	n/a	n/a
27	ARID3A	chr5:90561874-90562466	K562	blood:	n/a	n/a
28	CTCF	chr5:90562140-90562290	HMF	breast:	n/a	n/a
29	CTCF	chr5:90562040-90562190	HVMF	connective:	n/a	n/a
30	RUNX3	chr5:90562124-90562546	GM12878	blood:	n/a	n/a
31	JUND	chr5:90562008-90562538	SK-N-SH	brain:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493 chr5:90562317-90562328
32	MEF2A	chr5:90562032-90562689	SK-N-SH	brain:	n/a	chr5:90562330-90562351 chr5:90562336-90562347 chr5:90562337-90562346 chr5:90562252-90562267 chr5:90562332-90562353 chr5:90562332-90562353 chr5:90562330-90562351 chr5:90562334-90562350 chr5:90562330-90562351 chr5:90562334-90562349 chr5:90562333-90562348 chr5:90562333-90562349
33	MEF2A	chr5:90562027-90562624	SK-N-SH	brain:	n/a	chr5:90562330-90562351 chr5:90562336-90562347 chr5:90562337-90562346 chr5:90562252-90562267 chr5:90562332-90562353 chr5:90562332-90562353 chr5:90562330-90562351 chr5:90562334-90562350 chr5:90562330-90562351 chr5:90562334-90562349 chr5:90562333-90562348 chr5:90562333-90562349
34	MEF2C	chr5:90562038-90562654	GM12878	blood:	n/a	chr5:90562330-90562351 chr5:90562336-90562347 chr5:90562337-90562346 chr5:90562252-90562267 chr5:90562332-90562353 chr5:90562332-90562353 chr5:90562330-90562351 chr5:90562334-90562350 chr5:90562330-90562351 chr5:90562334-90562349 chr5:90562333-90562349
35	JUN	chr5:90561724-90563017	K562	blood:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493
36	FOSL1	chr5:90562002-90562580	HCT-116	colon:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493
37	CTCF	chr5:90562060-90562210	K562	blood:	n/a	n/a
38	JUN	chr5:90562173-90562506	K562	blood:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493
39	JUND	chr5:90561910-90562571	SK-N-SH	brain:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493 chr5:90562317-90562328
40	CTCF	chr5:90562160-90562310	HPAF	blood vessel:	n/a	n/a
41	CTCF	chr5:90562080-90562230	HCM	heart:	n/a	n/a
42	FOS	chr5:90562117-90562522	HUVEC	blood vessel:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562317-90562328 chr5:90562319-90562328 chr5:90562481-90562493
43	ATF3	chr5:90562101-90562612	HCT-116	colon:	n/a	n/a
44	CTCF	chr5:90562060-90562210	GM12873	blood:	n/a	n/a
45	CTCF	chr5:90562040-90562190	HEEpiC	esophagus:	n/a	n/a
46	JUND	chr5:90561884-90562589	HCT-116	colon:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493 chr5:90562317-90562328
47	FOS	chr5:90562135-90562592	MCF10A-Er-Src	breast:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562317-90562328 chr5:90562319-90562328 chr5:90562481-90562493
48	CTCF	chr5:90562040-90562190	RPTEC	kidney:	n/a	n/a
49	SP1	chr5:90561798-90562635	HCT-116	colon:	n/a	n/a
50	JUN	chr5:90562143-90562526	HUVEC	blood vessel:	n/a	chr5:90562317-90562329 chr5:90562319-90562327 chr5:90562320-90562327 chr5:90562318-90562328 chr5:90562319-90562328 chr5:90562481-90562493

No.	Distal block	Cell Line	Cell type
1	chr5:90559982..90565400-chr5:90570467..90573729,4	K562	blood:
2	chr5:90555805..90566288-chr5:90673548..90682139,22	K562	blood:
3	chr5:90560937..90569122-chr5:90675177..90680484,12	K562	blood:
4	chr5:90560764..90562482-chr5:90665678..90667594,2	K562	blood:

Variant related genes	Relation type
RNU4-90P	TF binding region
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10474341	0.91[ASN][1000 genomes]
rs12188638	0.91[ASN][1000 genomes]
rs12514996	0.82[ASN][1000 genomes]
rs12515116	0.85[ASN][1000 genomes]
rs12520306	0.91[ASN][1000 genomes]
rs12653995	0.96[ASN][1000 genomes]
rs12658748	0.86[ASN][1000 genomes]
rs16869618	0.91[ASN][1000 genomes]
rs56377435	1.00[ASN][1000 genomes]
rs56876862	0.84[ASN][1000 genomes]
rs58781250	0.90[ASN][1000 genomes]
rs72786311	0.91[ASN][1000 genomes]
rs72786312	0.85[ASN][1000 genomes]
rs72786318	0.91[ASN][1000 genomes]
rs72786321	0.96[ASN][1000 genomes]
rs72786324	0.96[ASN][1000 genomes]
rs72786325	0.96[ASN][1000 genomes]
rs72786326	0.96[ASN][1000 genomes]
rs72786329	0.96[ASN][1000 genomes]
rs72786331	1.00[ASN][1000 genomes]
rs72786332	1.00[ASN][1000 genomes]
rs72786338	1.00[ASN][1000 genomes]
rs72786350	0.95[ASN][1000 genomes]
rs72786353	0.90[ASN][1000 genomes]
rs72786354	0.90[ASN][1000 genomes]
rs9647558	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90561000-90564800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:90561400-90562200	Enhancers	Pancreas	Pancrea
3	chr5:90561400-90562200	Enhancers	Stomach Smooth Muscle	stomach
4	chr5:90561600-90562200	Enhancers	K562	blood
5	chr5:90561600-90562800	Enhancers	Colon Smooth Muscle	Colon
6	chr5:90561600-90562800	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr5:90561600-90562800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr5:90561800-90562400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr5:90561800-90562600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:90561800-90562600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr5:90561800-90562800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:90561800-90562800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:90561800-90562800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:90561800-90562800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr5:90561800-90562800	Enhancers	Fetal Heart	heart
16	chr5:90561800-90562800	Enhancers	Rectal Smooth Muscle	rectum
17	chr5:90561800-90562800	Enhancers	A549	lung
18	chr5:90561800-90562800	Enhancers	Hela-S3	cervix
19	chr5:90561800-90562800	Enhancers	NH-A	brain
20	chr5:90561800-90563000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:90562000-90562200	Enhancers	Thymus	Thymus
22	chr5:90562000-90562200	Flanking Active TSS	GM12878-XiMat	blood
23	chr5:90562000-90562400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:90562000-90562400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:90562000-90562400	Enhancers	Stomach Mucosa	stomach
26	chr5:90562000-90562400	Enhancers	HMEC	breast
27	chr5:90562000-90562600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:90562000-90562600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:90562000-90562600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr5:90562000-90562600	Enhancers	NHLF	lung
31	chr5:90562000-90562800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr5:90562000-90562800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:90562000-90562800	Enhancers	HSMM	muscle
34	chr5:90562000-90562800	Enhancers	HSMMtube	muscle
35	chr5:90562000-90562800	Enhancers	NHDF-Ad	bronchial
36	chr5:90562000-90562800	Enhancers	NHEK	skin
37	chr5:90562000-90562800	Enhancers	Osteobl	bone
38	chr5:90562000-90563000	Enhancers	HUVEC	blood vessel

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