Variant report

Variant	rs58481769
Chromosome Location	chr2:46622473-46622474
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	CHD2	chr2:46622365-46622503	GM12878	blood:	n/a	n/a
2	BATF	chr2:46622368-46622608	GM12878	blood:	n/a	n/a
3	MAFK	chr2:46622441-46622478	HepG2	liver:	n/a	n/a
4	EBF1	chr2:46622463-46622649	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr2:46622464-46622481	GM12878	blood:	n/a	n/a
6	BHLHE40	chr2:46622367-46622601	GM12878	blood:	n/a	n/a
7	EP300	chr2:46622358-46622474	GM12878	blood:	n/a	n/a
8	TEAD4	chr2:46621627-46622575	HepG2	liver:	n/a	n/a
9	HDAC2	chr2:46621708-46622546	HepG2	liver:	n/a	n/a
10	IKZF1	chr2:46622336-46622583	GM12878	blood:	n/a	n/a
11	RUNX3	chr2:46622176-46622710	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:46622386-46622501	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr2:46622329-46622650	MCF10A-Er-Src	breast:	n/a	n/a
14	RUNX3	chr2:46622275-46622653	GM12878	blood:	n/a	n/a
15	EP300	chr2:46622337-46622601	GM12878	blood:	n/a	n/a
16	MBD4	chr2:46621780-46622740	HepG2	liver:	n/a	n/a
17	FOXA2	chr2:46621406-46622512	HepG2	liver:	n/a	n/a
18	FOS	chr2:46622334-46622549	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPAS1-2	chr2:46622033-46622603	l_1826_chr2:46622032-46623205_thyroid

Variant related genes	Relation type
ENSG00000228100	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1109286	0.89[ASN][1000 genomes]
rs11675328	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686509	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686705	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11689649	0.80[EUR][1000 genomes]
rs11689694	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11689989	0.93[EUR][1000 genomes]
rs11690114	0.88[ASN][1000 genomes]
rs11691694	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11693596	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11693754	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530622	0.87[ASN][1000 genomes]
rs1900592	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35193335	0.99[ASN][1000 genomes]
rs4952823	0.92[ASN][1000 genomes]
rs55826825	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55864213	0.93[EUR][1000 genomes]
rs56058321	0.93[EUR][1000 genomes]
rs56140012	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62138871	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591548	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605241	0.96[EUR][1000 genomes]
rs9677412	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46613200-46644200	Weak transcription	Aorta	Aorta
2	chr2:46614600-46623000	Weak transcription	Esophagus	oesophagus
3	chr2:46615400-46624800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:46620200-46622800	Enhancers	Placenta	Placenta
5	chr2:46620400-46631600	Weak transcription	K562	blood
6	chr2:46620600-46622800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:46621200-46622600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:46621600-46622600	Flanking Active TSS	HepG2	liver
9	chr2:46621600-46622600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr2:46621600-46622800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr2:46621800-46622600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:46621800-46623000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:46622000-46623000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:46622200-46622800	Enhancers	NHEK	skin
15	chr2:46622200-46623400	Enhancers	HMEC	breast
16	chr2:46622400-46622600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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