Variant report

Variant	rs1553113
Chromosome Location	chr5:58338437-58338438
allele	A/C
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	MYC	chr5:58338010-58338854	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:58338365-58338840	Hela-S3	cervix:	n/a	n/a
3	JUND	chr5:58337914-58338444	SK-N-SH	brain:	n/a	chr5:58338202-58338212 chr5:58338202-58338212 chr5:58338202-58338212 chr5:58338203-58338211 chr5:58338202-58338212
4	MAX	chr5:58337966-58339092	A549	lung:	n/a	n/a
5	RXRA	chr5:58337880-58338471	SK-N-SH	brain:	n/a	n/a
6	CEBPB	chr5:58337918-58338442	A549	lung:	n/a	n/a
7	EP300	chr5:58337690-58338566	A549	lung:	n/a	n/a
8	NFIC	chr5:58337856-58339033	SK-N-SH	brain:	n/a	n/a
9	BCL3	chr5:58335000-58338690	A549	lung:	n/a	chr5:58335393-58335406 chr5:58336423-58336432 chr5:58335440-58335453
10	TBP	chr5:58338005-58338456	Hela-S3	cervix:	n/a	n/a
11	NR3C1	chr5:58338391-58338781	A549	lung:	n/a	chr5:58338597-58338611
12	FOSL2	chr5:58337956-58338515	SK-N-SH	brain:	n/a	chr5:58338202-58338212 chr5:58338202-58338212 chr5:58338202-58338212 chr5:58338203-58338211 chr5:58338202-58338212
13	GABPA	chr5:58338031-58338471	A549	lung:	n/a	n/a
14	TCF12	chr5:58337853-58338568	SK-N-SH	brain:	n/a	n/a
15	MYC	chr5:58337855-58338875	MCF10A-Er-Src	breast:	n/a	n/a
16	SP1	chr5:58331577-58338881	A549	lung:	n/a	chr5:58333512-58333519 chr5:58335988-58335997
17	MAX	chr5:58338052-58338794	Hela-S3	cervix:	n/a	n/a
18	FOSL2	chr5:58337512-58338854	A549	lung:	n/a	chr5:58338202-58338212 chr5:58338202-58338212 chr5:58338202-58338212 chr5:58338203-58338211 chr5:58338202-58338212
19	FOS	chr5:58338018-58338501	MCF10A-Er-Src	breast:	n/a	chr5:58338202-58338212 chr5:58338202-58338212 chr5:58338201-58338212 chr5:58338202-58338212 chr5:58338203-58338211 chr5:58338202-58338212
20	EP300	chr5:58337861-58338806	A549	lung:	n/a	n/a
21	PBX3	chr5:58337921-58338453	SK-N-SH	brain:	n/a	n/a
22	NR3C1	chr5:58338415-58338801	A549	lung:	n/a	chr5:58338597-58338611
23	REST	chr5:58337973-58338689	A549	lung:	n/a	n/a
24	USF2	chr5:58338434-58338619	Hela-S3	cervix:	n/a	n/a
25	SP1	chr5:58337906-58338856	A549	lung:	n/a	n/a
26	SMC3	chr5:58338008-58338743	Hela-S3	cervix:	n/a	n/a
27	NR3C1	chr5:58337967-58338892	A549	lung:	n/a	chr5:58338597-58338611 chr5:58338287-58338305 chr5:58338283-58338309
28	TCF12	chr5:58337846-58338996	SK-N-SH	brain:	n/a	n/a
29	TCF7L2	chr5:58337954-58338650	Hela-S3	cervix:	n/a	chr5:58338554-58338561 chr5:58338554-58338563
30	NR3C1	chr5:58338409-58338765	A549	lung:	n/a	chr5:58338597-58338611
31	GATA3	chr5:58330035-58338800	A549	lung:	n/a	chr5:58333570-58333591 chr5:58332852-58332859 chr5:58333577-58333587 chr5:58333577-58333584 chr5:58332250-58332259 chr5:58333577-58333584 chr5:58332852-58332859 chr5:58333577-58333584 chr5:58333572-58333588 chr5:58336798-58336814 chr5:58332852-58332859
32	MAX	chr5:58333100-58339130	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337561-58337571 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
33	GATA3	chr5:58337904-58338455	SK-N-SH	brain:	n/a	n/a
34	SIX5	chr5:58337263-58339081	A549	lung:	n/a	n/a
35	NR3C1	chr5:58337926-58338919	A549	lung:	n/a	chr5:58338597-58338611 chr5:58338287-58338305 chr5:58338283-58338309
36	POLR2A	chr5:58338160-58338994	A549	lung:	n/a	n/a
37	TCF12	chr5:58337764-58339073	A549	lung:	n/a	n/a
38	CHD2	chr5:58338057-58338869	Hela-S3	cervix:	n/a	n/a
39	FOS	chr5:58337959-58338857	MCF10A-Er-Src	breast:	n/a	chr5:58338202-58338212 chr5:58338202-58338212 chr5:58338201-58338212 chr5:58338202-58338212 chr5:58338203-58338211 chr5:58338202-58338212

Variant related genes	Relation type
PDE4D	TF binding region

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10940640	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1353747	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1498608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16889126	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17777413	0.87[EUR][1000 genomes]
rs2968010	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336000-58338600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:58336000-58343600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
4	chr5:58336400-58338600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr5:58336400-58338800	Enhancers	Stomach Mucosa	stomach
6	chr5:58336600-58339000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr5:58336600-58339000	Enhancers	Primary hematopoietic stem cells	blood
8	chr5:58336600-58339000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:58336600-58342000	Weak transcription	Pancreas	Pancrea
10	chr5:58336600-58348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:58336600-58351800	Weak transcription	Fetal Intestine Small	intestine
12	chr5:58336600-58358000	Weak transcription	Fetal Intestine Large	intestine
13	chr5:58336600-58358000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:58336800-58338600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr5:58336800-58338800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:58336800-58338800	Enhancers	HepG2	liver
17	chr5:58336800-58339000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr5:58337000-58338600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:58337000-58338800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:58337000-58338800	Flanking Active TSS	A549	lung
21	chr5:58337200-58338800	Enhancers	Fetal Thymus	thymus
22	chr5:58337200-58339000	Enhancers	NHEK	skin
23	chr5:58337400-58338800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:58337400-58339000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:58337400-58339000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:58337400-58339000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr5:58337400-58339000	Enhancers	HMEC	breast
28	chr5:58337400-58339000	Enhancers	NH-A	brain
29	chr5:58337400-58339200	Enhancers	Psoas Muscle	Psoas
30	chr5:58337400-58339200	Enhancers	HSMM	muscle
31	chr5:58337400-58359000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:58337600-58338800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:58337600-58338800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:58337600-58338800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:58337600-58338800	Enhancers	Osteobl	bone
36	chr5:58337600-58339000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:58337600-58339000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr5:58337600-58339000	Enhancers	HUVEC	blood vessel
39	chr5:58338000-58338600	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr5:58338000-58338600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:58338000-58338600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:58338000-58338800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:58338000-58338800	Enhancers	Fetal Muscle Leg	muscle
44	chr5:58338000-58339000	Enhancers	Fetal Heart	heart
45	chr5:58338000-58339000	Enhancers	Rectal Smooth Muscle	rectum
46	chr5:58338000-58339000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr5:58338200-58338600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:58338200-58338600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:58338200-58339000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:58338200-58339000	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links