Variant report

Variant	rs9293565
Chromosome Location	chr5:90609736-90609737
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	POLR2A	chr5:90609578-90610449	Hela-S3	cervix:	n/a	n/a
2	JUND	chr5:90609504-90610626	SK-N-SH	brain:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610262-90610273 chr5:90610264-90610272
3	NFIC	chr5:90609628-90610617	ECC-1	luminal epithelium:	n/a	n/a
4	GATA3	chr5:90609669-90610622	SK-N-SH	brain:	n/a	n/a
5	TCF7L2	chr5:90609654-90610484	PANC-1	pancreas:	n/a	chr5:90609654-90609663 chr5:90609655-90609662 chr5:90609655-90609665 chr5:90610263-90610272
6	TCF12	chr5:90609505-90610526	ECC-1	luminal epithelium:	n/a	n/a
7	TEAD4	chr5:90609570-90610585	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr5:90609538-90610668	SK-N-SH	brain:	n/a	n/a
9	EP300	chr5:90609563-90610668	ECC-1	luminal epithelium:	n/a	chr5:90610264-90610273 chr5:90610358-90610365
10	EP300	chr5:90609600-90610724	A549	lung:	n/a	chr5:90610264-90610273 chr5:90610358-90610365
11	SP1	chr5:90609626-90610753	HCT-116	colon:	n/a	n/a
12	REST	chr5:90609562-90610575	A549	lung:	n/a	n/a
13	EP300	chr5:90609498-90610744	SK-N-SH	brain:	n/a	chr5:90610264-90610273 chr5:90610358-90610365
14	POLR2A	chr5:90595038-90610657	U87	brain:	n/a	n/a
15	JUN	chr5:90609713-90610636	K562	blood:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610264-90610272
16	CBX3	chr5:90609675-90610592	HCT-116	colon:	n/a	n/a
17	POLR2A	chr5:90609617-90610520	Hela-S3	cervix:	n/a	n/a
18	FOXM1	chr5:90609537-90610565	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr5:90609560-90610598	A549	lung:	n/a	chr5:90610264-90610273
20	NFIC	chr5:90609681-90610616	SK-N-SH	brain:	n/a	n/a
21	SP1	chr5:90609656-90610755	HCT-116	colon:	n/a	n/a
22	FOXM1	chr5:90609559-90610652	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr5:90609586-90610500	Hela-S3	cervix:	n/a	n/a
24	TCF7L2	chr5:90609617-90610585	Hela-S3	cervix:	n/a	chr5:90609654-90609663 chr5:90609655-90609662 chr5:90609655-90609665 chr5:90610263-90610272
25	MAX	chr5:90609687-90610489	A549	lung:	n/a	chr5:90610264-90610273
26	TCF7L2	chr5:90609680-90610542	HCT-116	colon:	n/a	chr5:90610263-90610272
27	SIN3AK20	chr5:90609728-90610569	HCT-116	colon:	n/a	n/a
28	POLR2A	chr5:90596852-90610582	U87	brain:	n/a	n/a
29	ZKSCAN1	chr5:90609714-90610481	Hela-S3	cervix:	n/a	n/a
30	CEBPB	chr5:90609641-90610763	HCT-116	colon:	n/a	chr5:90610378-90610386
31	POLR2A	chr5:90606580-90610482	Hela-S3	cervix:	n/a	n/a
32	MAX	chr5:90609678-90610554	Hela-S3	cervix:	n/a	chr5:90610264-90610273
33	NR3C1	chr5:90609695-90610390	ECC-1	luminal epithelium:	n/a	n/a
34	JUND	chr5:90609606-90610676	HCT-116	colon:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610262-90610273 chr5:90610264-90610272
35	MAX	chr5:90609594-90610725	HCT-116	colon:	n/a	chr5:90610264-90610273
36	SIN3AK20	chr5:90609573-90610654	HCT-116	colon:	n/a	n/a
37	TEAD4	chr5:90609613-90610579	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr5:90609583-90610501	HCT-116	colon:	n/a	n/a
39	POLR2A	chr5:90609632-90610355	MCF10A-Er-Src	breast:	n/a	n/a
40	FOXM1	chr5:90609728-90610538	SK-N-SH	brain:	n/a	n/a
41	MXI1	chr5:90609696-90610515	Hela-S3	cervix:	n/a	n/a
42	ZNF263	chr5:90609613-90610512	HEK293-T-REx	kidney:	n/a	n/a
43	TCF12	chr5:90609588-90610675	ECC-1	luminal epithelium:	n/a	n/a
44	FOSL1	chr5:90609723-90610657	HCT-116	colon:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610262-90610273 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610264-90610272
45	EP300	chr5:90609716-90610613	A549	lung:	n/a	chr5:90610264-90610273 chr5:90610358-90610365
46	POLR2A	chr5:90604771-90610527	U87	brain:	n/a	n/a
47	CEBPB	chr5:90609717-90610541	ECC-1	luminal epithelium:	n/a	chr5:90610378-90610386
48	BCL3	chr5:90609580-90610653	A549	lung:	n/a	n/a
49	NFIC	chr5:90609544-90610591	ECC-1	luminal epithelium:	n/a	n/a
50	E2F6	chr5:90609725-90610552	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:156534984..156535558-chr5:90609305..90610027,2	Hela-S3	cervix:
2	chr5:90607284..90611861-chr5:90674569..90683045,11	K562	blood:
3	chr5:90575227..90576970-chr5:90607873..90610168,2	K562	blood:
4	chr5:90608430..90610124-chr5:90673476..90676069,2	K562	blood:
5	chr5:90607483..90611926-chr5:90672625..90681906,20	MCF-7	breast:
6	chr5:90608356..90610045-chr5:90671011..90673343,2	K562	blood:
7	chr5:90605667..90612137-chr5:90676262..90681561,13	K562	blood:
8	chr5:90574749..90579554-chr5:90606387..90610471,6	MCF-7	breast:
9	chr5:90607535..90610829-chr5:90673824..90679078,6	MCF-7	breast:
10	chr5:90576418..90578111-chr5:90608143..90610210,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARRDC3-1	chr5:90609455-90609850	NONHSAT102743

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

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10036206	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10038890	0.86[AFR][1000 genomes]
rs12697808	0.91[AFR][1000 genomes]
rs13176999	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941891	0.84[CHB][hapmap]
rs2941905	0.84[CHB][hapmap]
rs2973463	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs7727632	0.93[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90605400-90611200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr5:90605600-90610200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:90605800-90610400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:90605800-90610400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr5:90605800-90611200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:90606000-90611200	Enhancers	Fetal Thymus	thymus
7	chr5:90606400-90610400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:90606400-90610800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:90606600-90610400	Enhancers	Primary T cells from cord blood	blood
10	chr5:90606600-90610600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr5:90606600-90612200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:90606800-90609800	Enhancers	NHLF	lung
13	chr5:90606800-90610200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr5:90606800-90610600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:90606800-90611400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:90607000-90609800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:90607000-90610200	Enhancers	Thymus	Thymus
18	chr5:90607000-90610400	Enhancers	Fetal Muscle Leg	muscle
19	chr5:90607000-90610600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr5:90607200-90609800	Enhancers	Brain Anterior Caudate	brain
21	chr5:90607200-90610200	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr5:90607200-90610400	Enhancers	Brain Angular Gyrus	brain
23	chr5:90607200-90610600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr5:90607400-90610600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr5:90607400-90610600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr5:90607600-90609800	Enhancers	HepG2	liver
27	chr5:90607600-90609800	Enhancers	HMEC	breast
28	chr5:90607600-90609800	Enhancers	HUVEC	blood vessel
29	chr5:90607600-90610600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr5:90607600-90611400	Enhancers	K562	blood
31	chr5:90607800-90610600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr5:90607800-90610600	Enhancers	Rectal Smooth Muscle	rectum
33	chr5:90607800-90610600	Flanking Active TSS	Hela-S3	cervix
34	chr5:90607800-90611000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:90608000-90609800	Weak transcription	Stomach Mucosa	stomach
36	chr5:90608000-90610600	Enhancers	Fetal Heart	heart
37	chr5:90608000-90610800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr5:90608200-90609800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:90608200-90609800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:90608200-90609800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr5:90608200-90609800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:90608200-90609800	Enhancers	Dnd41	blood
43	chr5:90608200-90610000	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr5:90608200-90610000	Weak transcription	Placenta	Placenta
45	chr5:90608200-90610200	Active TSS	Psoas Muscle	Psoas
46	chr5:90608200-90610400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:90608200-90610600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:90608200-90610600	Enhancers	HSMM	muscle
49	chr5:90608400-90609800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:90608400-90609800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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