Variant report

Variant	rs13161074
Chromosome Location	chr5:178057466-178057467
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	FOSL2	chr5:178057266-178058037	HepG2	liver:	n/a	chr5:178058016-178058028 chr5:178058018-178058026 chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
2	E2F4	chr5:178057068-178057640	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr5:178057420-178057933	HepG2	liver:	n/a	chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
4	HDAC2	chr5:178057297-178057842	HepG2	liver:	n/a	chr5:178057569-178057578
5	CEBPB	chr5:178057356-178057925	HepG2	liver:	n/a	n/a
6	REST	chr5:178057411-178057904	HepG2	liver:	n/a	chr5:178057628-178057637
7	STAT3	chr5:178057436-178057802	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA2	chr5:178057459-178058028	A549	lung:	n/a	n/a
9	EP300	chr5:178057323-178057901	HepG2	liver:	n/a	chr5:178057568-178057578 chr5:178057663-178057670
10	GATA3	chr5:178057050-178058239	MCF-7	breast:	n/a	chr5:178057111-178057127 chr5:178057111-178057127
11	MAFK	chr5:178057374-178057913	HepG2	liver:	n/a	chr5:178057574-178057585
12	JUND	chr5:178057416-178058079	HCT-116	colon:	n/a	chr5:178058016-178058028 chr5:178058018-178058026 chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
13	GATA3	chr5:178057376-178057955	MCF-7	breast:	n/a	n/a
14	RFX5	chr5:178057396-178058090	HepG2	liver:	n/a	n/a
15	TCF7L2	chr5:178057445-178057934	HEK293	kidney:	n/a	chr5:178057600-178057609 chr5:178057597-178057613 chr5:178057597-178057613 chr5:178057599-178057609 chr5:178057597-178057611 chr5:178057598-178057612
16	FOSL2	chr5:178057366-178057981	MCF-7	breast:	n/a	chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
17	RCOR1	chr5:178057199-178058246	IMR90	lung:	n/a	n/a
18	FOXA1	chr5:178057365-178058015	HepG2	liver:	n/a	n/a
19	FOXA1	chr5:178057351-178058019	HepG2	liver:	n/a	n/a
20	CEBPB	chr5:178057390-178057898	HepG2	liver:	n/a	n/a
21	MAFK	chr5:178057383-178057966	HepG2	liver:	n/a	chr5:178057574-178057585
22	TCF12	chr5:178057332-178058051	A549	lung:	n/a	n/a
23	REST	chr5:178057420-178057898	MCF-7	breast:	n/a	chr5:178057628-178057637
24	GATA3	chr5:178057197-178058082	A549	lung:	n/a	n/a
25	POLR2A	chr5:178057326-178057666	MCF10A-Er-Src	breast:	n/a	n/a
26	CEBPB	chr5:178057431-178057715	HepG2	liver:	n/a	n/a
27	KAP1	chr5:178057368-178058195	HEK293	kidney:	n/a	n/a
28	MYBL2	chr5:178057249-178058076	HepG2	liver:	n/a	n/a
29	FOS	chr5:178057298-178057857	MCF10A-Er-Src	breast:	n/a	chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
30	NFIC	chr5:178057278-178057945	HepG2	liver:	n/a	n/a
31	CEBPB	chr5:178057390-178057985	MCF-7	breast:	n/a	n/a
32	HDAC2	chr5:178057323-178057975	HepG2	liver:	n/a	chr5:178057569-178057578
33	EP300	chr5:178057282-178058048	HepG2	liver:	n/a	chr5:178057568-178057578 chr5:178057663-178057670
34	MAZ	chr5:178057282-178058089	HepG2	liver:	n/a	n/a
35	MYBL2	chr5:178057299-178057954	HepG2	liver:	n/a	n/a
36	CREB1	chr5:178057322-178057919	HepG2	liver:	n/a	n/a
37	TCF7L2	chr5:178057349-178057963	MCF-7	breast:	n/a	chr5:178057600-178057609 chr5:178057597-178057613 chr5:178057597-178057613 chr5:178057599-178057609 chr5:178057597-178057611 chr5:178057598-178057612
38	EP300	chr5:178057370-178057820	HepG2	liver:	n/a	chr5:178057568-178057578 chr5:178057663-178057670
39	JUND	chr5:178057237-178058136	HepG2	liver:	n/a	chr5:178058016-178058028 chr5:178058018-178058026 chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
40	SIN3AK20	chr5:178057085-178058201	MCF-7	breast:	n/a	n/a
41	MAFF	chr5:178057371-178058094	HepG2	liver:	n/a	n/a
42	SMC3	chr5:178057418-178058062	HepG2	liver:	n/a	n/a
43	POLR2A	chr5:178057405-178058095	HepG2	liver:	n/a	n/a
44	FOSL1	chr5:178057314-178057941	HCT-116	colon:	n/a	chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
45	NR2F2	chr5:178057263-178058077	MCF-7	breast:	n/a	n/a
46	SP1	chr5:178057338-178057896	HepG2	liver:	n/a	n/a
47	FOXA1	chr5:178057264-178058014	HepG2	liver:	n/a	n/a
48	RCOR1	chr5:178057450-178058145	HepG2	liver:	n/a	n/a
49	HNF4A	chr5:178057442-178057918	HepG2	liver:	n/a	chr5:178057571-178057579
50	MAX	chr5:178057244-178058165	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178056292..178058896-chr5:178156268..178158313,2	MCF-7	breast:
2	chr5:178052987..178056050-chr5:178056072..178058258,3	MCF-7	breast:

Variant related genes	Relation type
CLK4	TF binding region
ENSG00000113240	Chromatin interaction
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10035557	0.83[ASN][1000 genomes]
rs10051137	0.83[ASN][1000 genomes]
rs10061455	0.85[ASN][1000 genomes]
rs10061883	0.86[ASN][1000 genomes]
rs10064009	0.86[ASN][1000 genomes]
rs10065419	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10070794	0.86[ASN][1000 genomes]
rs10073925	0.85[ASN][1000 genomes]
rs10479501	0.86[ASN][1000 genomes]
rs11742564	0.89[ASN][1000 genomes]
rs11744815	0.89[ASN][1000 genomes]
rs11748909	0.83[ASN][1000 genomes]
rs12654185	0.85[ASN][1000 genomes]
rs12654187	0.85[ASN][1000 genomes]
rs12719855	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13187977	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13360296	0.89[ASN][1000 genomes]
rs1472457	0.84[ASN][1000 genomes]
rs1967419	0.83[ASN][1000 genomes]
rs2335442	0.83[ASN][1000 genomes]
rs262021	0.83[ASN][1000 genomes]
rs262028	0.81[ASN][1000 genomes]
rs262036	0.83[ASN][1000 genomes]
rs388749	0.83[ASN][1000 genomes]
rs4073633	0.86[ASN][1000 genomes]
rs4077796	0.88[ASN][1000 genomes]
rs4079109	0.86[ASN][1000 genomes]
rs4079111	0.86[ASN][1000 genomes]
rs4079112	0.86[ASN][1000 genomes]
rs4301240	0.86[ASN][1000 genomes]
rs4413550	0.86[ASN][1000 genomes]
rs4418123	0.86[ASN][1000 genomes]
rs4437394	0.86[ASN][1000 genomes]
rs4521498	0.89[ASN][1000 genomes]
rs4976798	0.83[ASN][1000 genomes]
rs6600942	0.88[ASN][1000 genomes]
rs6866336	0.83[ASN][1000 genomes]
rs6866952	0.86[ASN][1000 genomes]
rs6869889	0.89[ASN][1000 genomes]
rs6871074	0.91[ASN][1000 genomes]
rs721142	0.83[ASN][1000 genomes]
rs721143	0.83[ASN][1000 genomes]
rs73353860	0.84[ASN][1000 genomes]
rs73353883	0.85[ASN][1000 genomes]
rs752043	0.83[ASN][1000 genomes]
rs7707891	0.91[ASN][1000 genomes]
rs7715291	0.83[ASN][1000 genomes]
rs7720708	0.83[ASN][1000 genomes]
rs7736565	0.83[ASN][1000 genomes]
rs776153	0.83[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13161074	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178054600-178057600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:178054600-178057800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:178054600-178058800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:178054600-178059200	Weak transcription	Right Atrium	heart
5	chr5:178054600-178061600	Weak transcription	HMEC	breast
6	chr5:178054800-178058000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:178055000-178057800	Weak transcription	Primary B cells from cord blood	blood
8	chr5:178057200-178058000	Enhancers	NHEK	skin
9	chr5:178057200-178058200	Flanking Active TSS	HepG2	liver
10	chr5:178057200-178058600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:178057400-178057800	Enhancers	K562	blood
12	chr5:178057400-178057800	Enhancers	NH-A	brain
13	chr5:178057400-178058000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:178057400-178058000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:178057400-178058000	Enhancers	Hela-S3	cervix
16	chr5:178057400-178058200	Enhancers	Osteobl	bone
17	chr5:178057400-178058600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr5:178057400-178058800	Enhancers	Primary B cells from peripheral blood	blood

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