Variant report

Variant	rs28489657
Chromosome Location	chr5:89705296-89705297
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:381)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:381 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr5:89704909-89706243	ECC-1	luminal epithelium:	n/a	n/a
2	REST	chr5:89704776-89706332	A549	lung:	n/a	n/a
3	POLR2A	chr5:89704651-89706358	ProgFib	skin:	n/a	n/a
4	ZBTB33	chr5:89704911-89705457	HepG2	liver:	n/a	chr5:89705166-89705181
5	BHLHE40	chr5:89704883-89706217	GM12878	blood:	n/a	n/a
6	SMC3	chr5:89705038-89706509	Hela-S3	cervix:	n/a	n/a
7	ATF2	chr5:89704762-89705527	GM12878	blood:	n/a	n/a
8	RELA	chr5:89704884-89706418	GM15510	blood:	n/a	n/a
9	ZBTB33	chr5:89704783-89706096	HCT-116	colon:	n/a	chr5:89705166-89705181
10	POLR2A	chr5:89704447-89706382	MCF-7	breast:	n/a	n/a
11	RFX5	chr5:89705096-89706104	HepG2	liver:	n/a	n/a
12	CEBPB	chr5:89704651-89706050	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr5:89704959-89706317	HepG2	liver:	n/a	n/a
14	RCOR1	chr5:89704914-89706347	HepG2	liver:	n/a	n/a
15	E2F6	chr5:89704920-89706297	A549	lung:	n/a	chr5:89705727-89705742 chr5:89705339-89705346 chr5:89705339-89705346 chr5:89705339-89705346 chr5:89705338-89705350 chr5:89705756-89705765
16	ELK1	chr5:89705178-89706413	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:89704816-89705720	SK-N-MC	brain:	n/a	n/a
18	MAFF	chr5:89705178-89706176	HepG2	liver:	n/a	n/a
19	TCF3	chr5:89705000-89705313	GM12878	blood:	n/a	n/a
20	ELF1	chr5:89705032-89706078	GM12878	blood:	n/a	chr5:89705576-89705588
21	MAFK	chr5:89705053-89706638	K562	blood:	n/a	n/a
22	STAT5A	chr5:89704635-89706259	GM12878	blood:	n/a	chr5:89705045-89705052
23	POLR2A	chr5:89704414-89706449	GM18505	blood:	n/a	n/a
24	POLR2A	chr5:89704554-89706200	HepG2	liver:	n/a	n/a
25	POLR2A	chr5:89704936-89706309	HL-60	blood:	n/a	n/a
26	MAX	chr5:89704876-89706325	ECC-1	luminal epithelium:	n/a	chr5:89705733-89705743
27	ZBTB33	chr5:89704950-89705505	GM12878	blood:	n/a	chr5:89705166-89705181
28	SIN3AK20	chr5:89704977-89705713	A549	lung:	n/a	n/a
29	POLR2A	chr5:89704710-89706371	U87	brain:	n/a	n/a
30	MAX	chr5:89704855-89706300	A549	lung:	n/a	chr5:89705733-89705743
31	POLR2A	chr5:89704332-89706845	K562	blood:	n/a	n/a
32	MTA3	chr5:89704881-89705683	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:89704622-89706280	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr5:89704467-89706697	GM12878	blood:	n/a	n/a
35	NFYA	chr5:89705006-89706167	Hela-S3	cervix:	n/a	n/a
36	CHD2	chr5:89704707-89706166	GM12878	blood:	n/a	chr5:89705168-89705177
37	POLR2A	chr5:89704542-89706373	HEK293	kidney:	n/a	n/a
38	TCF12	chr5:89704357-89706173	ECC-1	luminal epithelium:	n/a	n/a
39	STAT1	chr5:89704969-89706164	GM12878	blood:	n/a	chr5:89705045-89705052
40	POLR2A	chr5:89704818-89706632	HUVEC	blood vessel:	n/a	n/a
41	MAX	chr5:89704897-89705667	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr5:89704924-89705679	H1-hESC	embryonic stem cell:	n/a	n/a
43	FOXM1	chr5:89704801-89706171	GM12878	blood:	n/a	n/a
44	TAF1	chr5:89704884-89706178	K562	blood:	n/a	n/a
45	POLR2A	chr5:89704683-89706485	HCT-116	colon:	n/a	n/a
46	RFX5	chr5:89704885-89706408	Hela-S3	cervix:	n/a	n/a
47	REST	chr5:89704742-89705555	K562	blood:	n/a	n/a
48	POLR2A	chr5:89704993-89705636	HepG2	liver:	n/a	n/a
49	TEAD4	chr5:89704464-89705661	K562	blood:	n/a	n/a
50	BCLAF1	chr5:89704762-89705654	GM12878	blood:	n/a	chr5:89704915-89704924

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89680507..89687450-chr5:89698366..89705754,8	MCF-7	breast:
2	chr5:89701553..89708894-chr5:89768084..89771807,14	K562	blood:
3	chr5:89705209..89706757-chr5:89853526..89855162,2	MCF-7	breast:
4	chr13:27998631..27999207-chr5:89705029..89705899,2	NB4	blood:
5	chr5:89703250..89710229-chr5:89936398..89944611,13	K562	blood:
6	chr5:89684756..89687141-chr5:89703504..89706860,3	MCF-7	breast:
7	chr5:89703976..89707575-chr5:89854064..89857316,4	K562	blood:
8	chr5:89704960..89708059-chr5:89823269..89827144,6	K562	blood:
9	chr5:89703907..89705481-chr5:89717381..89719278,2	MCF-7	breast:
10	chr5:89705215..89707531-chr5:90675292..90676863,2	K562	blood:
11	chr5:89705290..89707109-chr5:89824364..89826854,3	MCF-7	breast:
12	chr5:89705042..89707173-chr5:90677000..90680355,4	K562	blood:
13	chr5:89704759..89705573-chr7:21466952..21467883,2	Hela-S3	cervix:
14	chr15:62682227..62682755-chr5:89705071..89706015,2	Hela-S3	cervix:
15	chr5:89704382..89708328-chr5:89852696..89856618,6	MCF-7	breast:
16	chr5:89704649..89705392-chr9:123604695..123605609,2	HCT-116	colon:
17	chr2:61763500..61764142-chr5:89704700..89705584,2	Hela-S3	cervix:
18	chr5:89703358..89707086-chr5:89823955..89827154,6	MCF-7	breast:
19	chr5:68530475..68532147-chr5:89705204..89707833,2	MCF-7	breast:
20	chr5:89702524..89708084-chr5:89764247..89773389,22	K562	blood:
21	chr5:88178723..88181688-chr5:89702719..89707070,5	K562	blood:
22	chr5:89701624..89708275-chr5:89936212..89939090,6	K562	blood:
23	chr5:89680611..89687152-chr5:89704124..89707534,9	K562	blood:
24	chr5:89705231..89707575-chr5:89854422..89857316,5	K562	blood:
25	chr5:89705095..89707110-chr5:90075841..90078344,2	K562	blood:
26	chr5:89703591..89705335-chr6:26204580..26206448,2	K562	blood:
27	chr5:89703407..89707223-chr5:89822965..89826833,10	K562	blood:
28	chr5:89705215..89707825-chr5:90675292..90676863,3	K562	blood:
29	chr5:89705130..89705748-chr6:151186281..151187109,2	Hela-S3	cervix:
30	chr5:89703543..89706963-chr5:89767513..89771420,6	MCF-7	breast:
31	chr5:89703949..89706595-chr5:90076409..90078344,2	K562	blood:
32	chr5:89704232..89708009-chr5:90677895..90680741,3	K562	blood:
33	chr5:89705255..89705991-chr5:89825165..89825777,2	NB4	blood:
34	chr5:89704491..89706992-chr5:89769088..89771566,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255647	TF binding region
CETN3	TF binding region
ENSG00000176018	Chromatin interaction
ENSG00000095261	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000226752	Chromatin interaction
ENSG00000260871	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000120254	Chromatin interaction
ENSG00000105866	Chromatin interaction
ENSG00000082898	Chromatin interaction
ENSG00000122034	Chromatin interaction
ENSG00000081189	Chromatin interaction
ENSG00000248309	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000171914	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10474326	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12109087	1.00[EUR][1000 genomes]
rs13355867	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13356310	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13361468	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16868673	1.00[EUR][1000 genomes]
rs28513348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28604505	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28710856	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28869620	1.00[EUR][1000 genomes]
rs6882045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9293544	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882363	chr5:89643399-89725515	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89703000-89707600	Active TSS	GM12878-XiMat	blood
2	chr5:89703200-89706800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr5:89703200-89707200	Active TSS	K562	blood
4	chr5:89704200-89706400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:89704200-89706800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:89704200-89706800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr5:89704200-89706800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:89704200-89706800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:89704200-89706800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:89704200-89706800	Active TSS	Fetal Brain Female	brain
11	chr5:89704200-89706800	Active TSS	NHEK	skin
12	chr5:89704200-89707000	Active TSS	A549	lung
13	chr5:89704200-89707000	Active TSS	NHLF	lung
14	chr5:89704400-89706400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr5:89704400-89706600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:89704400-89706600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:89704400-89706600	Active TSS	Psoas Muscle	Psoas
18	chr5:89704400-89706600	Active TSS	HSMM	muscle
19	chr5:89704400-89706800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr5:89704400-89706800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:89704400-89706800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:89704400-89706800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:89704400-89706800	Active TSS	Fetal Kidney	kidney
24	chr5:89704400-89706800	Active TSS	Right Ventricle	heart
25	chr5:89704400-89707000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:89704600-89706200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:89704600-89706200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:89704600-89706400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:89704600-89706400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:89704600-89706400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:89704600-89706400	Active TSS	Esophagus	oesophagus
32	chr5:89704600-89706400	Active TSS	Left Ventricle	heart
33	chr5:89704600-89706400	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr5:89704600-89706600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:89704600-89706600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:89704600-89706600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:89704600-89706600	Active TSS	Brain Germinal Matrix	brain
38	chr5:89704600-89706600	Active TSS	Fetal Muscle Trunk	muscle
39	chr5:89704600-89706600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr5:89704600-89706800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:89704600-89706800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:89704600-89706800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:89704600-89706800	Active TSS	Aorta	Aorta
44	chr5:89704600-89707000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:89704600-89707000	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr5:89704600-89707000	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr5:89704600-89707000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:89704600-89707200	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr5:89704800-89706200	Active TSS	Brain Hippocampus Middle	brain
50	chr5:89704800-89706400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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