Variant report

Variant	rs9596305
Chromosome Location	chr13:51103502-51103503
allele	A/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	STAT3	chr13:51103179-51104037	MCF10A-Er-Src	breast:	n/a	chr13:51103427-51103438
2	STAT3	chr13:51103219-51103762	MCF10A-Er-Src	breast:	n/a	chr13:51103427-51103438
3	KAP1	chr13:51102984-51104076	HEK293	kidney:	n/a	n/a
4	TCF7L2	chr13:51102991-51104257	HEK293	kidney:	n/a	chr13:51103946-51103960
5	JUND	chr13:51103429-51103516	K562	blood:	n/a	n/a
6	POLR2A	chr13:51103325-51103651	SK-N-SH	brain:	n/a	n/a
7	STAT3	chr13:51103130-51104012	MCF10A-Er-Src	breast:	n/a	chr13:51103427-51103438
8	STAT3	chr13:51103115-51103981	MCF10A-Er-Src	breast:	n/a	chr13:51103427-51103438
9	NR3C1	chr13:51103423-51103754	A549	lung:	n/a	chr13:51103572-51103579
10	POLR2A	chr13:51103183-51103942	U87	brain:	n/a	n/a
11	FOS	chr13:51103252-51103926	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr13:51103338-51104102	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr13:51103391-51103949	Gliobla	brain:	n/a	n/a
14	POLR2A	chr13:51103396-51103851	HCT-116	colon:	n/a	n/a
15	RAD21	chr13:51103342-51103929	IMR90	lung:	n/a	chr13:51103629-51103643
16	TEAD4	chr13:51103394-51104006	ECC-1	luminal epithelium:	n/a	n/a
17	TCF12	chr13:51103348-51103998	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr13:51103102-51104007	U87	brain:	n/a	n/a
19	ZNF263	chr13:51102956-51104131	HEK293-T-REx	kidney:	n/a	n/a
20	POLR2A	chr13:51103096-51104013	U87	brain:	n/a	n/a
21	NFIC	chr13:51103179-51103924	SK-N-SH	brain:	n/a	n/a
22	REST	chr13:51103482-51103915	MCF-7	breast:	n/a	n/a
23	TCF7L2	chr13:51103244-51104138	PANC-1	pancreas:	n/a	chr13:51103946-51103960
24	RAD21	chr13:51103233-51103831	SK-N-SH_RA	brain:	n/a	chr13:51103629-51103643
25	MAX	chr13:51103331-51103959	ECC-1	luminal epithelium:	n/a	n/a
26	MYC	chr13:51103345-51103815	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr13:51103183-51103923	U87	brain:	n/a	n/a
28	NFIC	chr13:51103204-51104191	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr13:51103314-51103898	ProgFib	skin:	n/a	n/a
30	YY1	chr13:51103454-51103879	ECC-1	luminal epithelium:	n/a	n/a
31	NFIC	chr13:51103331-51104021	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr13:51103244-51103891	ECC-1	luminal epithelium:	n/a	n/a
33	SETDB1	chr13:51103322-51103947	U2OS	brain:	n/a	n/a
34	POLR2A	chr13:51103356-51103893	PANC-1	pancreas:	n/a	n/a
35	CTCF	chr13:51103440-51103590	HCM	heart:	n/a	n/a
36	FOS	chr13:51103256-51103793	MCF10A-Er-Src	breast:	n/a	n/a
37	E2F4	chr13:51103220-51103743	MCF10A-Er-Src	breast:	n/a	chr13:51103636-51103645
38	MYC	chr13:51103377-51103904	MCF10A-Er-Src	breast:	n/a	n/a
39	TCF7L2	chr13:51103225-51104143	HCT-116	colon:	n/a	chr13:51103946-51103960
40	YY1	chr13:51103408-51103896	ECC-1	luminal epithelium:	n/a	n/a
41	KAP1	chr13:51103181-51104037	U2OS	brain:	n/a	n/a
42	POLR2A	chr13:51103253-51103980	HUVEC	blood vessel:	n/a	n/a
43	SP1	chr13:51103132-51104138	HCT-116	colon:	n/a	n/a
44	FOS	chr13:51103227-51103816	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr13:51103287-51103820	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr13:51103321-51104065	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50699976..50701803-chr13:51102949..51104727,2	MCF-7	breast:
2	chr13:50698015..50701526-chr13:51100615..51103673,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNASEH2B-3	chr13:51102316-51104215	NONHSAT033842

Variant related genes	Relation type
ENSG00000229323	TF binding region
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12584983	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17074530	0.83[ASN][1000 genomes]
rs17074548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201748	0.82[ASN][1000 genomes]
rs2148936	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286658	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs279077	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs59806618	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60462956	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9596303	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51099800-51104000	Enhancers	Fetal Muscle Leg	muscle
2	chr13:51099800-51104000	Enhancers	Fetal Thymus	thymus
3	chr13:51099800-51104000	Enhancers	Thymus	Thymus
4	chr13:51100000-51105200	Enhancers	Primary T cells from cord blood	blood
5	chr13:51100400-51105200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr13:51100600-51103800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr13:51100600-51103800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr13:51100600-51104000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr13:51100600-51104200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr13:51100800-51103800	Enhancers	Primary hematopoietic stem cells	blood
11	chr13:51100800-51104200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr13:51101000-51103800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:51101200-51103600	Enhancers	Colon Smooth Muscle	Colon
14	chr13:51101600-51104000	Enhancers	Fetal Kidney	kidney
15	chr13:51102000-51103600	Enhancers	HMEC	breast
16	chr13:51102000-51103600	Enhancers	HSMMtube	muscle
17	chr13:51102000-51103800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr13:51102000-51104000	Enhancers	A549	lung
19	chr13:51102000-51106000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:51102200-51103600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:51102200-51103600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr13:51102200-51104000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr13:51102200-51104000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr13:51102200-51106000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr13:51102400-51103600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr13:51102400-51103800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr13:51102400-51104200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr13:51102800-51103600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr13:51102800-51103800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:51102800-51103800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr13:51102800-51104000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:51102800-51104400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:51103000-51103600	Enhancers	Fetal Muscle Trunk	muscle
34	chr13:51103000-51103600	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr13:51103000-51103600	Enhancers	NH-A	brain
36	chr13:51103000-51103800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr13:51103000-51103800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr13:51103000-51103800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr13:51103000-51104000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr13:51103000-51104000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:51103000-51104000	Enhancers	Placenta	Placenta
42	chr13:51103000-51104000	Flanking Active TSS	Dnd41	blood
43	chr13:51103000-51104200	Enhancers	Stomach Mucosa	stomach
44	chr13:51103200-51103600	Enhancers	K562	blood
45	chr13:51103200-51103800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr13:51103200-51103800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr13:51103200-51103800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr13:51103200-51103800	Enhancers	Esophagus	oesophagus
49	chr13:51103200-51103800	Enhancers	Pancreas	Pancrea
50	chr13:51103200-51104000	Enhancers	H1 Cell Line	embryonic stem cell

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