Variant report

Variant	rs12521927
Chromosome Location	chr5:35617594-35617595
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	MAX	chr5:35617505-35618398	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZKSCAN1	chr5:35617419-35618622	Hela-S3	cervix:	n/a	n/a
3	E2F6	chr5:35617440-35618157	A549	lung:	n/a	chr5:35617796-35617808
4	MAFK	chr5:35617428-35618158	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:35617577-35618214	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr5:35617543-35618289	ECC-1	luminal epithelium:	n/a	chr5:35618210-35618226
7	RPC155	chr5:35617225-35617940	Hela-S3	cervix:	n/a	n/a
8	KAP1	chr5:35617580-35618183	U2OS	brain:	n/a	n/a
9	NFYA	chr5:35617581-35618050	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:35617516-35618615	PBDE	blood:	n/a	n/a
11	CREB1	chr5:35617449-35618175	A549	lung:	n/a	n/a
12	CTCF	chr5:35617574-35617615	GM19238	blood:	n/a	n/a
13	CTCF	chr5:35617567-35618160	A549	lung:	n/a	chr5:35617896-35617904 chr5:35617893-35617906 chr5:35617895-35617916 chr5:35617893-35617911 chr5:35617893-35617906 chr5:35617894-35617910
14	CTCF	chr5:35617555-35617595	Fibrobl	skin:	n/a	n/a
15	MAX	chr5:35617497-35618255	A549	lung:	n/a	n/a
16	CTCF	chr5:35617548-35617628	NHEK	skin:	n/a	n/a
17	POLR2A	chr5:35617288-35618253	HL-60	blood:	n/a	n/a
18	MAX	chr5:35617358-35618721	A549	lung:	n/a	n/a
19	CTCF	chr5:35617552-35617683	Spleen_OC	spleen:	n/a	n/a
20	POLR2A	chr5:35617496-35618179	U87	brain:	n/a	n/a
21	NRF1	chr5:35617543-35618397	SK-N-SH	brain:	n/a	chr5:35617867-35617881 chr5:35617864-35617878 chr5:35618244-35618253
22	CTCF	chr5:35617580-35617730	GM12870	blood:	n/a	n/a
23	MXI1	chr5:35617503-35618702	IMR90	lung:	n/a	n/a
24	SIN3AK20	chr5:35617499-35618458	HCT-116	colon:	n/a	n/a
25	CTCF	chr5:35617045-35618789	A549	lung:	n/a	chr5:35617896-35617904 chr5:35617893-35617906 chr5:35617895-35617916 chr5:35617893-35617911 chr5:35617893-35617906 chr5:35617894-35617910
26	SIN3AK20	chr5:35617491-35618674	MCF-7	breast:	n/a	n/a
27	TBP	chr5:35617453-35618115	Hela-S3	cervix:	n/a	n/a
28	MAZ	chr5:35617347-35618585	IMR90	lung:	n/a	n/a
29	CREB1	chr5:35617486-35618136	H1-hESC	embryonic stem cell:	n/a	n/a
30	HCFC1	chr5:35616998-35619378	Hela-S3	cervix:	n/a	n/a
31	GTF2F1	chr5:35617438-35618140	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr5:35617392-35618287	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr5:35617491-35618616	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr5:35617448-35618476	Hela-S3	cervix:	n/a	n/a
35	MAX	chr5:35617546-35618112	A549	lung:	n/a	n/a
36	RCOR1	chr5:35617440-35618577	Hela-S3	cervix:	n/a	n/a
37	CHD2	chr5:35617442-35618515	Hela-S3	cervix:	n/a	chr5:35618252-35618262
38	MXI1	chr5:35617585-35618391	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr5:35617514-35618179	U87	brain:	n/a	n/a
40	POLR2A	chr5:35617398-35618433	GM19099	blood:	n/a	n/a
41	SMARCB1	chr5:35617522-35618567	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr5:35617590-35618087	ProgFib	skin:	n/a	chr5:35617896-35617904 chr5:35617893-35617906 chr5:35617895-35617916 chr5:35617893-35617911 chr5:35617893-35617906 chr5:35617894-35617910
43	GTF3C2	chr5:35617299-35617894	Hela-S3	cervix:	n/a	n/a
44	SMC3	chr5:35617424-35618765	SK-N-SH	brain:	n/a	chr5:35617895-35617909
45	MAX	chr5:35617444-35618706	Hela-S3	cervix:	n/a	n/a
46	TCF12	chr5:35617501-35618236	ECC-1	luminal epithelium:	n/a	n/a
47	RAD21	chr5:35617537-35618141	Hela-S3	cervix:	n/a	chr5:35617894-35617913 chr5:35617895-35617904 chr5:35617895-35617909 chr5:35617893-35617907
48	POLR2A	chr5:35617492-35617611	A549	lung:	n/a	n/a
49	TCF12	chr5:35617485-35618474	ECC-1	luminal epithelium:	n/a	n/a
50	RAD21	chr5:35617588-35618153	ECC-1	luminal epithelium:	n/a	chr5:35617894-35617913 chr5:35617895-35617904 chr5:35617895-35617909 chr5:35617893-35617907

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21458436..21458960-chr5:35617140..35617799,2	Hela-S3	cervix:

Variant related genes	Relation type
SPEF2	TF binding region

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

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

rs_ID	r²[population]
rs12514911	0.96[EUR][1000 genomes]
rs1508662	0.89[EUR][1000 genomes]
rs1605677	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs286441	1.00[EUR][1000 genomes]
rs406830	1.00[EUR][1000 genomes]
rs430828	1.00[EUR][1000 genomes]
rs60139581	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6878233	0.89[EUR][1000 genomes]
rs73091428	0.89[EUR][1000 genomes]
rs7700662	1.00[EUR][1000 genomes]
rs7725149	0.89[EUR][1000 genomes]
rs7735024	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525477	chr5:35530905-35792990	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35616800-35619400	Flanking Active TSS	Dnd41	blood
2	chr5:35617200-35617600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr5:35617200-35617800	Active TSS	Primary B cells from cord blood	blood
4	chr5:35617200-35617800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr5:35617200-35618200	Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr5:35617200-35618400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:35617200-35618400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr5:35617200-35618400	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr5:35617200-35618400	Active TSS	Osteobl	bone
10	chr5:35617200-35618600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:35617200-35618600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:35617200-35618600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:35617200-35618600	Active TSS	Fetal Kidney	kidney
14	chr5:35617200-35618600	Active TSS	Monocytes-CD14+_RO01746	blood
15	chr5:35617200-35618800	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr5:35617200-35618800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:35617200-35618800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:35617200-35618800	Active TSS	A549	lung
19	chr5:35617200-35618800	Active TSS	HMEC	breast
20	chr5:35617200-35618800	Active TSS	NHDF-Ad	bronchial
21	chr5:35617400-35617600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:35617400-35617600	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr5:35617400-35617600	Active TSS	Primary hematopoietic stem cells	blood
24	chr5:35617400-35617600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:35617400-35617600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:35617400-35617600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr5:35617400-35617600	Enhancers	Placenta	Placenta
28	chr5:35617400-35617600	Enhancers	Placenta Amnion	Placenta Amnion
29	chr5:35617400-35617800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:35617400-35617800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr5:35617400-35617800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr5:35617400-35617800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:35617400-35617800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:35617400-35617800	Active TSS	Liver	Liver
35	chr5:35617400-35617800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr5:35617400-35617800	Flanking Active TSS	HepG2	liver
37	chr5:35617400-35618000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:35617400-35618000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:35617400-35618000	Active TSS	Adipose Nuclei	Adipose
40	chr5:35617400-35618000	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr5:35617400-35618000	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr5:35617400-35618200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:35617400-35618200	Active TSS	Primary T cells from cord blood	blood
44	chr5:35617400-35618200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:35617400-35618200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:35617400-35618200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:35617400-35618200	Active TSS	Colonic Mucosa	Colon
48	chr5:35617400-35618200	Active TSS	Fetal Muscle Leg	muscle
49	chr5:35617400-35618200	Active TSS	Left Ventricle	heart
50	chr5:35617400-35618200	Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links