Variant report

Variant	rs2115501
Chromosome Location	chr5:89769999-89770000
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	SIN3AK20	chr5:89769506-89771120	HCT-116	colon:	n/a	n/a
2	STAT3	chr5:89769977-89770077	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF143	chr5:89769847-89770989	K562	blood:	n/a	chr5:89770361-89770371 chr5:89770210-89770228
4	STAT5A	chr5:89769874-89770240	GM12878	blood:	n/a	n/a
5	USF2	chr5:89769785-89770079	Hela-S3	cervix:	n/a	n/a
6	SP1	chr5:89769624-89771184	A549	lung:	n/a	chr5:89770632-89770644 chr5:89770239-89770249 chr5:89770655-89770665 chr5:89770654-89770666 chr5:89770634-89770643 chr5:89770655-89770665 chr5:89770633-89770642 chr5:89770858-89770871 chr5:89770651-89770665 chr5:89770656-89770665 chr5:89770654-89770666 chr5:89770629-89770643 chr5:89770633-89770643 chr5:89770632-89770644 chr5:89770893-89770900 chr5:89770655-89770664 chr5:89770633-89770643
7	KAP1	chr5:89768970-89771055	HEK293	kidney:	n/a	n/a
8	TBP	chr5:89768894-89771288	Hela-S3	cervix:	n/a	n/a
9	MYC	chr5:89769676-89770792	MCF-7	breast:	n/a	chr5:89770655-89770665 chr5:89770234-89770244
10	POLR2A	chr5:89769382-89771008	A549	lung:	n/a	n/a
11	CHD2	chr5:89769920-89770955	H1-hESC	embryonic stem cell:	n/a	n/a
12	TBP	chr5:89769047-89770954	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F1	chr5:89769562-89770892	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr5:89769692-89771020	HUVEC	blood vessel:	n/a	n/a
15	ETS1	chr5:89769514-89770836	K562	blood:	n/a	chr5:89770234-89770245
16	PAX5	chr5:89769813-89770915	GM12878	blood:	n/a	n/a
17	RCOR1	chr5:89769944-89770978	HepG2	liver:	n/a	n/a
18	CREB1	chr5:89769747-89770881	H1-hESC	embryonic stem cell:	n/a	n/a
19	USF2	chr5:89769623-89770058	GM12878	blood:	n/a	n/a
20	MYC	chr5:89769674-89770953	HepG2	liver:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
21	ATF2	chr5:89769870-89770838	GM12878	blood:	n/a	n/a
22	HEY1	chr5:89769659-89770955	K562	blood:	n/a	n/a
23	TAF1	chr5:89769959-89770887	GM12878	blood:	n/a	n/a
24	TRIM28	chr5:89769856-89770965	K562	blood:	n/a	n/a
25	PAX5	chr5:89769558-89770934	GM12892	blood:	n/a	n/a
26	POLR2A	chr5:89769089-89770975	NB4	blood:	n/a	n/a
27	NFATC1	chr5:89769952-89770747	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:89769432-89771148	PFSK-1	brain:	n/a	n/a
29	HCFC1	chr5:89769470-89771033	K562	blood:	n/a	n/a
30	MAZ	chr5:89769006-89771106	IMR90	lung:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
31	BACH1	chr5:89769103-89771002	H1-hESC	embryonic stem cell:	n/a	n/a
32	EGR1	chr5:89769270-89770930	HCT-116	colon:	n/a	chr5:89770237-89770246 chr5:89770234-89770248 chr5:89770650-89770663 chr5:89770651-89770662 chr5:89770515-89770522 chr5:89770650-89770663 chr5:89770649-89770664 chr5:89770514-89770529 chr5:89770514-89770528 chr5:89770234-89770247 chr5:89770234-89770247 chr5:89770234-89770247 chr5:89770655-89770665 chr5:89770235-89770246 chr5:89770233-89770248 chr5:89770234-89770247 chr5:89770515-89770528 chr5:89770139-89770149 chr5:89770515-89770528 chr5:89770230-89770252 chr5:89770650-89770664
33	RCOR1	chr5:89769068-89771039	Hela-S3	cervix:	n/a	n/a
34	E2F6	chr5:89769070-89771102	K562	blood:	n/a	n/a
35	TEAD4	chr5:89769605-89770940	ECC-1	luminal epithelium:	n/a	n/a
36	JUND	chr5:89769959-89771091	H1-hESC	embryonic stem cell:	n/a	n/a
37	MYC	chr5:89769545-89770885	K562	blood:	n/a	chr5:89770655-89770665 chr5:89770234-89770244
38	CBX3	chr5:89769768-89771020	HCT-116	colon:	n/a	n/a
39	PAX5	chr5:89769929-89770904	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:89769878-89770869	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr5:89769058-89770947	K562	blood:	n/a	n/a
42	EGR1	chr5:89769718-89770844	ECC-1	luminal epithelium:	n/a	chr5:89770237-89770246 chr5:89770234-89770248 chr5:89770650-89770663 chr5:89770651-89770662 chr5:89770515-89770522 chr5:89770650-89770663 chr5:89770649-89770664 chr5:89770514-89770529 chr5:89770514-89770528 chr5:89770234-89770247 chr5:89770234-89770247 chr5:89770234-89770247 chr5:89770655-89770665 chr5:89770235-89770246 chr5:89770233-89770248 chr5:89770234-89770247 chr5:89770515-89770528 chr5:89770139-89770149 chr5:89770515-89770528 chr5:89770230-89770252 chr5:89770650-89770664
43	CREB1	chr5:89769518-89770905	A549	lung:	n/a	n/a
44	ZBTB7A	chr5:89769906-89771228	ECC-1	luminal epithelium:	n/a	n/a
45	EGR1	chr5:89769632-89770963	K562	blood:	n/a	chr5:89770237-89770246 chr5:89770234-89770248 chr5:89770650-89770663 chr5:89770651-89770662 chr5:89770515-89770522 chr5:89770650-89770663 chr5:89770649-89770664 chr5:89770514-89770529 chr5:89770514-89770528 chr5:89770234-89770247 chr5:89770234-89770247 chr5:89770234-89770247 chr5:89770655-89770665 chr5:89770235-89770246 chr5:89770233-89770248 chr5:89770234-89770247 chr5:89770515-89770528 chr5:89770139-89770149 chr5:89770515-89770528 chr5:89770230-89770252 chr5:89770650-89770664
46	CHD2	chr5:89769110-89770896	K562	blood:	n/a	n/a
47	POLR2A	chr5:89769898-89770954	U87	brain:	n/a	n/a
48	POLR2A	chr5:89769032-89771013	K562	blood:	n/a	n/a
49	ELF1	chr5:89769913-89770925	GM12878	blood:	n/a	n/a
50	MAX	chr5:89769021-89771203	HepG2	liver:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907

No.	Distal block	Cell Line	Cell type
1	chr5:89769889..89770559-chrX:48754652..48755367,2	Hela-S3	cervix:
2	chr5:89769110..89772331-chr5:90086907..90091587,4	K562	blood:
3	chr5:89769550..89772254-chr5:89851679..89856622,6	MCF-7	breast:
4	chr5:89769761..89770604-chr7:104653040..104653631,2	Hela-S3	cervix:
5	chr1:210547411..210548099-chr5:89769614..89770507,2	Hela-S3	cervix:
6	chr5:89704491..89706992-chr5:89769088..89771566,3	MCF-7	breast:
7	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
8	chr5:89702524..89708084-chr5:89764247..89773389,22	K562	blood:
9	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:
10	chr5:89768685..89771799-chr5:89852676..89855842,6	MCF-7	breast:
11	chr5:89768584..89771978-chr5:90675764..90678297,3	K562	blood:
12	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
13	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
14	chr5:89764343..89768380-chr5:89768675..89771583,10	MCF-7	breast:
15	chr5:89701553..89708894-chr5:89768084..89771807,14	K562	blood:
16	chr5:89769970..89770696-chr8:144349534..144350176,2	HCT-116	colon:
17	chr5:89769121..89772256-chr5:89935164..89938437,4	K562	blood:
18	chr5:89703543..89706963-chr5:89767513..89771420,6	MCF-7	breast:

Variant related genes	Relation type
POLR3G	TF binding region
ENSG00000126768	Chromatin interaction
ENSG00000102103	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000250571	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10054133	0.91[EUR][1000 genomes]
rs10473933	0.81[EUR][1000 genomes]
rs10474325	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11744529	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11953190	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11958751	0.82[YRI][hapmap]
rs2963695	0.95[EUR][1000 genomes]
rs2972966	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4129345	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs4131978	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57443165	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6884579	0.86[ASW][hapmap];0.91[CEU][hapmap];0.83[MKK][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes]
rs72781070	0.95[EUR][1000 genomes]
rs72781074	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv518131	chr5:89748142-89781594	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 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	chr5:89768200-89771400	Active TSS	GM12878-XiMat	blood
2	chr5:89768400-89770200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:89768400-89770400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr5:89768400-89771200	Active TSS	Brain Angular Gyrus	brain
5	chr5:89768600-89770000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:89768600-89770000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:89768600-89770800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:89768600-89771200	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr5:89768600-89771600	Active TSS	NHDF-Ad	bronchial
10	chr5:89768600-89772000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:89768800-89770000	Flanking Active TSS	Liver	Liver
12	chr5:89768800-89770200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr5:89768800-89770200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:89768800-89770200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr5:89768800-89770400	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr5:89768800-89770400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr5:89768800-89770800	Active TSS	NHLF	lung
18	chr5:89768800-89771200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:89768800-89771200	Active TSS	Fetal Heart	heart
20	chr5:89768800-89771200	Active TSS	Ovary	ovary
21	chr5:89768800-89771400	Active TSS	Fetal Intestine Large	intestine
22	chr5:89768800-89771400	Active TSS	A549	lung
23	chr5:89768800-89771600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:89768800-89771600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr5:89768800-89772000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr5:89768800-89773200	Active TSS	H9 Cell Line	embryonic stem cell
27	chr5:89768800-89773400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:89769000-89770000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr5:89769000-89770000	Flanking Active TSS	K562	blood
30	chr5:89769000-89770200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr5:89769000-89770200	Flanking Active TSS	Colonic Mucosa	Colon
32	chr5:89769000-89770400	Flanking Active TSS	Lung	lung
33	chr5:89769000-89770400	Bivalent/Poised TSS	HepG2	liver
34	chr5:89769000-89770800	Active TSS	Fetal Intestine Small	intestine
35	chr5:89769000-89770800	Active TSS	Gastric	stomach
36	chr5:89769000-89770800	Active TSS	Stomach Mucosa	stomach
37	chr5:89769000-89771000	Active TSS	Pancreas	Pancrea
38	chr5:89769000-89771200	Active TSS	Esophagus	oesophagus
39	chr5:89769000-89771200	Active TSS	Fetal Kidney	kidney
40	chr5:89769000-89771200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr5:89769000-89771600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:89769000-89772000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr5:89769000-89772400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:89769200-89770200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr5:89769200-89770200	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr5:89769200-89770200	Flanking Active TSS	Placenta	Placenta
47	chr5:89769200-89770400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr5:89769200-89770600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:89769200-89771000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:89769200-89771000	Active TSS	Small Intestine	intestine

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