Variant report

Variant	rs7518648
Chromosome Location	chr1:171313741-171313742
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	STAT3	chr1:171313715-171313981	MCF10A-Er-Src	breast:	n/a	chr1:171313823-171313831
2	RXRA	chr1:171313727-171313916	HepG2	liver:	n/a	chr1:171313841-171313855
3	EP300	chr1:171313709-171313935	HepG2	liver:	n/a	chr1:171313801-171313815
4	FOS	chr1:171313222-171313983	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr1:171313290-171313991	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:171313731-171313940	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr1:171313729-171313987	MCF10A-Er-Src	breast:	n/a	chr1:171313823-171313831
8	HNF4G	chr1:171313602-171313993	HepG2	liver:	n/a	chr1:171313841-171313854 chr1:171313839-171313854 chr1:171313840-171313854 chr1:171313841-171313853 chr1:171313841-171313853 chr1:171313839-171313854 chr1:171313840-171313853 chr1:171313838-171313856 chr1:171313841-171313853
9	SMC3	chr1:171313694-171313924	HepG2	liver:	n/a	n/a
10	ARID3A	chr1:171313681-171314019	HepG2	liver:	n/a	n/a
11	CEBPD	chr1:171313693-171313929	HepG2	liver:	n/a	n/a
12	STAT3	chr1:171313702-171314007	MCF10A-Er-Src	breast:	n/a	chr1:171313823-171313831
13	NFIC	chr1:171313639-171313927	HepG2	liver:	n/a	n/a
14	HNF4G	chr1:171313536-171314108	HepG2	liver:	n/a	chr1:171313841-171313854 chr1:171313839-171313854 chr1:171313840-171313854 chr1:171313841-171313853 chr1:171313841-171313853 chr1:171313839-171313854 chr1:171313840-171313853 chr1:171313838-171313856 chr1:171313841-171313853
15	MYC	chr1:171313320-171313972	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr1:171313578-171314025	HepG2	liver:	n/a	chr1:171313802-171313813 chr1:171313821-171313832 chr1:171313800-171313813 chr1:171313800-171313811
17	POLR2A	chr1:171313674-171313874	MCF10A-Er-Src	breast:	n/a	n/a
18	CEBPB	chr1:171313648-171313945	A549	lung:	n/a	chr1:171313802-171313813 chr1:171313821-171313832 chr1:171313800-171313813 chr1:171313800-171313811
19	CEBPB	chr1:171313640-171314003	HepG2	liver:	n/a	chr1:171313802-171313813 chr1:171313821-171313832 chr1:171313800-171313813 chr1:171313800-171313811
20	HNF4A	chr1:171313703-171313923	HepG2	liver:	n/a	chr1:171313841-171313854 chr1:171313839-171313854 chr1:171313839-171313854 chr1:171313840-171313854 chr1:171313841-171313853 chr1:171313841-171313853 chr1:171313839-171313854 chr1:171313840-171313853 chr1:171313838-171313856 chr1:171313841-171313853
21	SP1	chr1:171313602-171314014	HepG2	liver:	n/a	n/a
22	CEBPB	chr1:171313671-171313951	HepG2	liver:	n/a	chr1:171313802-171313813 chr1:171313821-171313832 chr1:171313800-171313813 chr1:171313800-171313811
23	FOXA1	chr1:171313577-171314009	HepG2	liver:	n/a	n/a
24	HNF4A	chr1:171313626-171313952	HepG2	liver:	n/a	chr1:171313841-171313854 chr1:171313839-171313854 chr1:171313839-171313854 chr1:171313840-171313854 chr1:171313841-171313853 chr1:171313841-171313853 chr1:171313839-171313854 chr1:171313840-171313853 chr1:171313838-171313856 chr1:171313841-171313853
25	CEBPB	chr1:171313586-171313995	HepG2	liver:	n/a	chr1:171313802-171313813 chr1:171313821-171313832 chr1:171313800-171313813 chr1:171313800-171313811

Variant related genes	Relation type
ENSG00000225704	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10157634	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1018390	0.83[ASN][1000 genomes]
rs1018392	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1024171	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1024173	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1042772	0.93[ASN][1000 genomes]
rs10912810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912830	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912833	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912842	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11807475	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12057885	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12064618	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12121479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564530	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12735239	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12736204	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12737633	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747017	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1963273	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2011345	0.90[ASN][1000 genomes]
rs2011548	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2143090	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2179375	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2223477	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2235508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235511	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34668298	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35062585	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36112567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4615872	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916225	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6425167	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425192	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425194	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6656117	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656219	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6662297	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6667507	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6670432	0.90[ASN][1000 genomes]
rs6670627	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688317	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6699676	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67595287	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71573031	0.89[ASN][1000 genomes]
rs7516677	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7519001	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548166	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555359	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980120	0.89[ASN][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1002423	chr1:171294384-171376936	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv548188	chr1:171308832-171371998	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7518648	FMO4	cis	Artery Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171284200-171313800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:171299800-171314200	Weak transcription	Aorta	Aorta
3	chr1:171305600-171315200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:171312400-171314400	Enhancers	Fetal Intestine Small	intestine
5	chr1:171312800-171315600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:171313000-171313800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:171313000-171313800	Flanking Active TSS	Liver	Liver
8	chr1:171313000-171313800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:171313000-171314200	Enhancers	HepG2	liver
10	chr1:171313000-171314600	Enhancers	Fetal Intestine Large	intestine
11	chr1:171313200-171313800	Active TSS	Duodenum Mucosa	Duodenum
12	chr1:171313400-171313800	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:171313600-171313800	Enhancers	Right Ventricle	heart

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