Variant report

Variant	rs11746942
Chromosome Location	chr5:178057915-178057916
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	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	JUND	chr5:178057420-178057933	HepG2	liver:	n/a	chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
3	CEBPB	chr5:178057356-178057925	HepG2	liver:	n/a	n/a
4	FOXA2	chr5:178057459-178058028	A549	lung:	n/a	n/a
5	GATA3	chr5:178057050-178058239	MCF-7	breast:	n/a	chr5:178057111-178057127 chr5:178057111-178057127
6	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
7	GATA3	chr5:178057376-178057955	MCF-7	breast:	n/a	n/a
8	RFX5	chr5:178057396-178058090	HepG2	liver:	n/a	n/a
9	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
10	FOSL2	chr5:178057366-178057981	MCF-7	breast:	n/a	chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
11	RCOR1	chr5:178057199-178058246	IMR90	lung:	n/a	n/a
12	FOXA1	chr5:178057365-178058015	HepG2	liver:	n/a	n/a
13	FOXA1	chr5:178057351-178058019	HepG2	liver:	n/a	n/a
14	MAFK	chr5:178057383-178057966	HepG2	liver:	n/a	chr5:178057574-178057585
15	TCF12	chr5:178057332-178058051	A549	lung:	n/a	n/a
16	GATA3	chr5:178057197-178058082	A549	lung:	n/a	n/a
17	KAP1	chr5:178057368-178058195	HEK293	kidney:	n/a	n/a
18	MYBL2	chr5:178057249-178058076	HepG2	liver:	n/a	n/a
19	NFIC	chr5:178057278-178057945	HepG2	liver:	n/a	n/a
20	MAX	chr5:178057546-178057999	HepG2	liver:	n/a	n/a
21	CEBPB	chr5:178057390-178057985	MCF-7	breast:	n/a	n/a
22	HDAC2	chr5:178057323-178057975	HepG2	liver:	n/a	chr5:178057569-178057578
23	EP300	chr5:178057282-178058048	HepG2	liver:	n/a	chr5:178057568-178057578 chr5:178057663-178057670
24	HEY1	chr5:178057713-178058031	HepG2	liver:	n/a	n/a
25	MAZ	chr5:178057282-178058089	HepG2	liver:	n/a	n/a
26	MYBL2	chr5:178057299-178057954	HepG2	liver:	n/a	n/a
27	CREB1	chr5:178057322-178057919	HepG2	liver:	n/a	n/a
28	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
29	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
30	SIN3AK20	chr5:178057085-178058201	MCF-7	breast:	n/a	n/a
31	MAFF	chr5:178057371-178058094	HepG2	liver:	n/a	n/a
32	SMC3	chr5:178057418-178058062	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:178057405-178058095	HepG2	liver:	n/a	n/a
34	FOSL1	chr5:178057314-178057941	HCT-116	colon:	n/a	chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
35	NR2F2	chr5:178057263-178058077	MCF-7	breast:	n/a	n/a
36	FOXA1	chr5:178057264-178058014	HepG2	liver:	n/a	n/a
37	RCOR1	chr5:178057450-178058145	HepG2	liver:	n/a	n/a
38	HNF4A	chr5:178057442-178057918	HepG2	liver:	n/a	chr5:178057571-178057579
39	MAX	chr5:178057244-178058165	MCF-7	breast:	n/a	n/a
40	TCF7L2	chr5:178057422-178057950	HCT-116	colon:	n/a	chr5:178057600-178057609 chr5:178057597-178057613 chr5:178057597-178057613 chr5:178057599-178057609 chr5:178057597-178057611 chr5:178057598-178057612
41	FOXA1	chr5:178057271-178058037	HepG2	liver:	n/a	n/a
42	FOSL2	chr5:178057367-178058137	HepG2	liver:	n/a	chr5:178058016-178058028 chr5:178058018-178058026 chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
43	TEAD4	chr5:178057290-178057995	HepG2	liver:	n/a	n/a
44	NR2F2	chr5:178057286-178058014	MCF-7	breast:	n/a	n/a
45	ARID3A	chr5:178057206-178058255	HepG2	liver:	n/a	n/a
46	FOSL2	chr5:178057370-178057980	A549	lung:	n/a	chr5:178057738-178057746 chr5:178057734-178057745 chr5:178057558-178057568 chr5:178057558-178057568
47	TBP	chr5:178057427-178058140	HepG2	liver:	n/a	n/a
48	FOXA2	chr5:178057397-178057968	HepG2	liver:	n/a	n/a
49	MBD4	chr5:178057333-178057993	HepG2	liver:	n/a	n/a
50	KAP1	chr5:178057345-178058112	U2OS	brain:	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: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10063220	0.83[ASN][1000 genomes]
rs11249553	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11249554	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11249556	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11737903	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747742	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514311	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12518589	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13155255	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13156622	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35460909	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35522922	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36008351	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3925518	0.83[ASN][1000 genomes]
rs4079110	0.82[ASN][1000 genomes]
rs4587090	0.82[ASN][1000 genomes]
rs4976738	0.83[ASN][1000 genomes]
rs4976800	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs501721	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs519984	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs530542	0.87[EUR][1000 genomes]
rs574103	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs576097	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs584415	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs596780	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs602019	0.87[ASN][1000 genomes]
rs602451	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs643936	0.87[EUR][1000 genomes]
rs649585	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6863876	0.81[ASN][1000 genomes]
rs6865775	0.83[ASN][1000 genomes]
rs6882079	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6883747	0.83[ASN][1000 genomes]
rs6886390	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6890632	0.83[ASN][1000 genomes]
rs721144	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7702727	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9329045	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
rs11746942	CLK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178054600-178058800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:178054600-178059200	Weak transcription	Right Atrium	heart
3	chr5:178054600-178061600	Weak transcription	HMEC	breast
4	chr5:178054800-178058000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:178057200-178058000	Enhancers	NHEK	skin
6	chr5:178057200-178058200	Flanking Active TSS	HepG2	liver
7	chr5:178057200-178058600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:178057400-178058000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:178057400-178058000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:178057400-178058000	Enhancers	Hela-S3	cervix
11	chr5:178057400-178058200	Enhancers	Osteobl	bone
12	chr5:178057400-178058600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr5:178057400-178058800	Enhancers	Primary B cells from peripheral blood	blood
14	chr5:178057600-178058200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:178057800-178058000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:178057800-178058200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:178057800-178058200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr5:178057800-178059000	Enhancers	Primary B cells from cord blood	blood

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