Variant report

Variant	rs28369128
Chromosome Location	chr5:90610393-90610394
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	TEAD4	chr5:90610030-90610492	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:90610222-90610423	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr5:90609578-90610449	Hela-S3	cervix:	n/a	n/a
4	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
5	NFIC	chr5:90609628-90610617	ECC-1	luminal epithelium:	n/a	n/a
6	GATA3	chr5:90609669-90610622	SK-N-SH	brain:	n/a	n/a
7	CEBPB	chr5:90610035-90610541	A549	lung:	n/a	chr5:90610378-90610386
8	TCF7L2	chr5:90609654-90610484	PANC-1	pancreas:	n/a	chr5:90609654-90609663 chr5:90609655-90609662 chr5:90609655-90609665 chr5:90610263-90610272
9	TBL1XR1	chr5:90609966-90610454	K562	blood:	n/a	n/a
10	TCF12	chr5:90609505-90610526	ECC-1	luminal epithelium:	n/a	n/a
11	TBP	chr5:90609951-90610447	HepG2	liver:	n/a	n/a
12	TBP	chr5:90609796-90610520	Hela-S3	cervix:	n/a	n/a
13	TEAD4	chr5:90609570-90610585	ECC-1	luminal epithelium:	n/a	n/a
14	ZNF384	chr5:90610104-90610635	K562	blood:	n/a	n/a
15	TCF12	chr5:90609538-90610668	SK-N-SH	brain:	n/a	n/a
16	IRF1	chr5:90610064-90610464	K562	blood:	n/a	n/a
17	EP300	chr5:90609563-90610668	ECC-1	luminal epithelium:	n/a	chr5:90610264-90610273 chr5:90610358-90610365
18	CEBPB	chr5:90609808-90610664	HCT-116	colon:	n/a	chr5:90610378-90610386
19	GATA2	chr5:90609905-90610523	SH-SY5Y	brain:	n/a	n/a
20	RAD21	chr5:90609963-90610474	SK-N-SH_RA	brain:	n/a	n/a
21	EP300	chr5:90609600-90610724	A549	lung:	n/a	chr5:90610264-90610273 chr5:90610358-90610365
22	SIN3AK20	chr5:90609935-90610535	MCF-7	breast:	n/a	n/a
23	REST	chr5:90610086-90610443	K562	blood:	n/a	n/a
24	JUND	chr5:90609801-90610540	Hela-S3	cervix:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610262-90610273 chr5:90610264-90610272
25	SP1	chr5:90609626-90610753	HCT-116	colon:	n/a	n/a
26	ZNF217	chr5:90610069-90610484	MCF-7	breast:	n/a	n/a
27	ATF3	chr5:90610101-90610396	K562	blood:	n/a	n/a
28	FOSL1	chr5:90610095-90610457	K562	blood:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610262-90610273 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610264-90610272
29	MAX	chr5:90609961-90610517	SK-N-SH	brain:	n/a	chr5:90610264-90610273
30	EP300	chr5:90609787-90610529	Hela-S3	cervix:	n/a	chr5:90610264-90610273 chr5:90610358-90610365
31	TAL1	chr5:90609901-90610518	K562	blood:	n/a	n/a
32	RFX5	chr5:90610114-90610438	HepG2	liver:	n/a	n/a
33	FOXA1	chr5:90609977-90610492	HepG2	liver:	n/a	n/a
34	FOS	chr5:90609842-90610528	MCF10A-Er-Src	breast:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610264-90610272
35	CEBPB	chr5:90609974-90610555	Hela-S3	cervix:	n/a	chr5:90610378-90610386
36	HDAC2	chr5:90610020-90610512	MCF-7	breast:	n/a	n/a
37	REST	chr5:90609562-90610575	A549	lung:	n/a	n/a
38	EP300	chr5:90609498-90610744	SK-N-SH	brain:	n/a	chr5:90610264-90610273 chr5:90610358-90610365
39	FOXA1	chr5:90610107-90610402	HepG2	liver:	n/a	n/a
40	POLR2A	chr5:90595038-90610657	U87	brain:	n/a	n/a
41	TAF1	chr5:90609949-90610488	Hela-S3	cervix:	n/a	n/a
42	JUND	chr5:90609836-90610514	SK-N-SH	brain:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610262-90610273 chr5:90610264-90610272
43	USF1	chr5:90610051-90610481	A549	lung:	n/a	n/a
44	MAX	chr5:90609955-90610497	MCF-7	breast:	n/a	chr5:90610264-90610273
45	STAT5A	chr5:90609919-90610614	K562	blood:	n/a	n/a
46	RAD21	chr5:90609928-90610534	A549	lung:	n/a	n/a
47	JUN	chr5:90609713-90610636	K562	blood:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610264-90610272
48	RXRA	chr5:90609920-90610643	SK-N-SH	brain:	n/a	n/a
49	MAFK	chr5:90610073-90610617	HepG2	liver:	n/a	chr5:90610428-90610439 chr5:90610428-90610444 chr5:90610428-90610439 chr5:90610429-90610440 chr5:90610427-90610441 chr5:90610429-90610440 chr5:90610265-90610274 chr5:90610264-90610274
50	FOSL1	chr5:90610037-90610503	K562	blood:	n/a	chr5:90610264-90610272 chr5:90610264-90610271 chr5:90610262-90610273 chr5:90610263-90610273 chr5:90610262-90610274 chr5:90610264-90610272

No.	Distal block	Cell Line	Cell type
1	chr5:90609791..90613058-chr5:90669226..90672505,3	MCF-7	breast:
2	chr5:90607284..90611861-chr5:90674569..90683045,11	K562	blood:
3	chr5:90607483..90611926-chr5:90672625..90681906,20	MCF-7	breast:
4	chr5:90605667..90612137-chr5:90676262..90681561,13	K562	blood:
5	chr5:90574749..90579554-chr5:90606387..90610471,6	MCF-7	breast:
6	chr5:90607535..90610829-chr5:90673824..90679078,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271762	TF binding region
LUCAT1	TF binding region
ENSG00000113369	Chromatin interaction
ENSG00000234292	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12658394	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34107416	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56876862	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57859727	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58781250	0.90[ASN][1000 genomes]
rs67220802	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67863612	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888057	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786350	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72786353	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72786354	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72786358	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786359	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72786360	0.97[EUR][1000 genomes];1.00[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:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90605400-90611200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr5:90605800-90610400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr5:90605800-90610400	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr5:90605800-90611200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:90606000-90611200	Enhancers	Fetal Thymus	thymus
6	chr5:90606400-90610400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:90606400-90610800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:90606600-90610400	Enhancers	Primary T cells from cord blood	blood
9	chr5:90606600-90610600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr5:90606600-90612200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:90606800-90610600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:90606800-90611400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:90607000-90610400	Enhancers	Fetal Muscle Leg	muscle
14	chr5:90607000-90610600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:90607200-90610400	Enhancers	Brain Angular Gyrus	brain
16	chr5:90607200-90610600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr5:90607400-90610600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr5:90607400-90610600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr5:90607600-90610600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr5:90607600-90611400	Enhancers	K562	blood
21	chr5:90607800-90610600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr5:90607800-90610600	Enhancers	Rectal Smooth Muscle	rectum
23	chr5:90607800-90610600	Flanking Active TSS	Hela-S3	cervix
24	chr5:90607800-90611000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:90608000-90610600	Enhancers	Fetal Heart	heart
26	chr5:90608000-90610800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:90608200-90610400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:90608200-90610600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:90608200-90610600	Enhancers	HSMM	muscle
30	chr5:90608400-90611200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:90608600-90610600	Enhancers	NHEK	skin
32	chr5:90608800-90610400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:90609000-90610400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:90609000-90611200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:90609000-90611200	Enhancers	H9 Cell Line	embryonic stem cell
36	chr5:90609200-90610400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr5:90609200-90610400	Enhancers	Colon Smooth Muscle	Colon
38	chr5:90609200-90612000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr5:90609400-90610400	Weak transcription	Lung	lung
40	chr5:90609400-90610600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:90609600-90610400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr5:90609600-90610400	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr5:90609600-90610400	Enhancers	Brain Cingulate Gyrus	brain
44	chr5:90609600-90610400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:90609600-90610400	Enhancers	Small Intestine	intestine
46	chr5:90609600-90610400	Enhancers	GM12878-XiMat	blood
47	chr5:90609600-90610600	Enhancers	Brain Substantia Nigra	brain
48	chr5:90609600-90610600	Flanking Active TSS	HSMMtube	muscle
49	chr5:90609600-90610800	Enhancers	Primary B cells from peripheral blood	blood
50	chr5:90609600-90611400	Enhancers	HUES6 Cell Line	embryonic stem cell

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