Variant report

Variant	rs56876862
Chromosome Location	chr5:90608789-90608790
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:90606789-90608835	MCF10A-Er-Src	breast:	n/a	n/a
2	TEAD4	chr5:90608351-90608854	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr5:90608421-90608831	HCT-116	colon:	n/a	n/a
4	RCOR1	chr5:90608570-90609107	K562	blood:	n/a	n/a
5	POLR2A	chr5:90595038-90610657	U87	brain:	n/a	n/a
6	POLR2A	chr5:90604813-90609443	U87	brain:	n/a	n/a
7	ZNF143	chr5:90608548-90608897	K562	blood:	n/a	n/a
8	RCOR1	chr5:90608511-90609046	K562	blood:	n/a	n/a
9	MAX	chr5:90606927-90609466	A549	lung:	n/a	n/a
10	TCF12	chr5:90607081-90609494	A549	lung:	n/a	n/a
11	POLR2A	chr5:90596852-90610582	U87	brain:	n/a	n/a
12	SP1	chr5:90607002-90608950	HCT-116	colon:	n/a	n/a
13	POLR2A	chr5:90606580-90610482	Hela-S3	cervix:	n/a	n/a
14	FOSL2	chr5:90607225-90609135	A549	lung:	n/a	n/a
15	RCOR1	chr5:90608555-90609225	Hela-S3	cervix:	n/a	n/a
16	ZNF143	chr5:90608650-90608877	Hela-S3	cervix:	n/a	n/a
17	EP300	chr5:90607117-90608825	A549	lung:	n/a	n/a
18	POLR2A	chr5:90607078-90609477	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:90604771-90610527	U87	brain:	n/a	n/a
20	MAX	chr5:90608607-90609452	A549	lung:	n/a	n/a
21	POLR2A	chr5:90608437-90608806	Hela-S3	cervix:	n/a	n/a
22	RCOR1	chr5:90607062-90609423	IMR90	lung:	n/a	n/a
23	POLR2A	chr5:90596037-90609349	A549	lung:	n/a	n/a
24	POLR2A	chr5:90606798-90610471	IMR90	lung:	n/a	n/a
25	EP300	chr5:90608700-90608812	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:90608764-90609391	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:90607284..90611861-chr5:90674569..90683045,11	K562	blood:
2	chr5:90575227..90576970-chr5:90607873..90610168,2	K562	blood:
3	chr5:90608430..90610124-chr5:90673476..90676069,2	K562	blood:
4	chr5:90607483..90611926-chr5:90672625..90681906,20	MCF-7	breast:
5	chr5:90608356..90610045-chr5:90671011..90673343,2	K562	blood:
6	chr5:90605667..90612137-chr5:90676262..90681561,13	K562	blood:
7	chr5:90574749..90579554-chr5:90606387..90610471,6	MCF-7	breast:
8	chr5:90607535..90610829-chr5:90673824..90679078,6	MCF-7	breast:
9	chr5:90576418..90578111-chr5:90608143..90610210,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARRDC3-1	chr5:90608717-90609046	XLOC_004924
2	lnc-GPR98-2	chr5:90608491-90609286	XLOC_004468

No data

Variant related genes	Relation type
LUCAT1	TF binding region
ENSG00000234292	Chromatin interaction
ENSG00000113369	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12653995	0.81[ASN][1000 genomes]
rs12658394	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28369128	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34107416	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56316727	0.84[ASN][1000 genomes]
rs56377435	0.84[ASN][1000 genomes]
rs57859727	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58781250	0.95[ASN][1000 genomes]
rs67220802	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67863612	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6888057	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72786321	0.81[ASN][1000 genomes]
rs72786324	0.81[ASN][1000 genomes]
rs72786325	0.81[ASN][1000 genomes]
rs72786326	0.81[ASN][1000 genomes]
rs72786329	0.81[ASN][1000 genomes]
rs72786331	0.84[ASN][1000 genomes]
rs72786332	0.84[ASN][1000 genomes]
rs72786338	0.84[ASN][1000 genomes]
rs72786350	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72786353	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72786354	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72786358	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72786359	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72786360	0.97[EUR][1000 genomes];0.95[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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90605200-90609000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr5:90605400-90611200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr5:90605600-90610200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:90605800-90610400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr5:90605800-90610400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr5:90605800-90611200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:90606000-90611200	Enhancers	Fetal Thymus	thymus
8	chr5:90606400-90609400	Enhancers	Lung	lung
9	chr5:90606400-90610400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:90606400-90610800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:90606600-90609000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:90606600-90610400	Enhancers	Primary T cells from cord blood	blood
13	chr5:90606600-90610600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr5:90606600-90612200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:90606800-90609400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr5:90606800-90609800	Enhancers	NHLF	lung
17	chr5:90606800-90610200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr5:90606800-90610600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:90606800-90611400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:90607000-90608800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:90607000-90609000	Enhancers	Brain Hippocampus Middle	brain
22	chr5:90607000-90609000	Transcr. at gene 5' and 3'	A549	lung
23	chr5:90607000-90609600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr5:90607000-90609800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:90607000-90610200	Enhancers	Thymus	Thymus
26	chr5:90607000-90610400	Enhancers	Fetal Muscle Leg	muscle
27	chr5:90607000-90610600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:90607200-90609200	Enhancers	Brain Substantia Nigra	brain
29	chr5:90607200-90609200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr5:90607200-90609800	Enhancers	Brain Anterior Caudate	brain
31	chr5:90607200-90610200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr5:90607200-90610400	Enhancers	Brain Angular Gyrus	brain
33	chr5:90607200-90610600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr5:90607400-90608800	Enhancers	Fetal Kidney	kidney
35	chr5:90607400-90610600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr5:90607400-90610600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr5:90607600-90609600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr5:90607600-90609800	Enhancers	HepG2	liver
39	chr5:90607600-90609800	Enhancers	HMEC	breast
40	chr5:90607600-90609800	Enhancers	HUVEC	blood vessel
41	chr5:90607600-90610600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr5:90607600-90611400	Enhancers	K562	blood
43	chr5:90607800-90609000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr5:90607800-90609000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:90607800-90609200	Weak transcription	Spleen	Spleen
46	chr5:90607800-90610600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr5:90607800-90610600	Enhancers	Rectal Smooth Muscle	rectum
48	chr5:90607800-90610600	Flanking Active TSS	Hela-S3	cervix
49	chr5:90607800-90611000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr5:90608000-90608800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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