Variant report

Variant	rs7723644
Chromosome Location	chr5:108260127-108260128
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	CTCF	chr5:108260103-108260309	K562	blood:	n/a	chr5:108260220-108260238
2	CTCF	chr5:108260100-108260250	AG09309	skin:	n/a	chr5:108260220-108260238
3	CTCF	chr5:108260063-108260334	H1-hESC	embryonic stem cell:	n/a	chr5:108260220-108260238
4	CTCF	chr5:108260080-108260230	RPTEC	kidney:	n/a	n/a
5	CBX3	chr5:108259973-108260635	HCT-116	colon:	n/a	n/a
6	RAD21	chr5:108259957-108260593	HCT-116	colon:	n/a	n/a
7	CTCF	chr5:108260120-108260270	HCM	heart:	n/a	chr5:108260220-108260238
8	RAD21	chr5:108260089-108260512	HepG2	liver:	n/a	n/a
9	CTCF	chr5:108260060-108260210	HUVEC	blood vessel:	n/a	n/a
10	MBD4	chr5:108260107-108260552	HepG2	liver:	n/a	n/a
11	RAD21	chr5:108260071-108260374	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr5:108260120-108260325	Hela-S3	cervix:	n/a	chr5:108260220-108260238
13	RAD21	chr5:108259975-108260565	HCT-116	colon:	n/a	n/a
14	SMC3	chr5:108260108-108260530	GM12878	blood:	n/a	n/a
15	CTCF	chr5:108260127-108260318	GM12878	blood:	n/a	chr5:108260220-108260238
16	TBL1XR1	chr5:108260110-108260632	K562	blood:	n/a	n/a
17	CTCF	chr5:108260120-108260270	GM12866	blood:	n/a	chr5:108260220-108260238
18	RAD21	chr5:108260070-108260374	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr5:108260074-108260334	HepG2	liver:	n/a	chr5:108260220-108260238
20	SP2	chr5:108260018-108260500	HepG2	liver:	n/a	n/a
21	CTCF	chr5:108260127-108260329	K562	blood:	n/a	chr5:108260220-108260238
22	CTCF	chr5:108260018-108260471	MCF-7	breast:	n/a	chr5:108260220-108260238
23	RAD21	chr5:108260048-108260449	H1-hESC	embryonic stem cell:	n/a	n/a
24	MYBL2	chr5:108259945-108260567	HepG2	liver:	n/a	n/a
25	CTCF	chr5:108260060-108260210	HRE	kidney:	n/a	n/a
26	RAD21	chr5:108260068-108260403	ECC-1	luminal epithelium:	n/a	n/a
27	CTCF	chr5:108259986-108260562	HCT-116	colon:	n/a	chr5:108260551-108260559 chr5:108260220-108260238
28	CTCFL	chr5:108260114-108260286	K562	blood:	n/a	n/a
29	CTCF	chr5:108260100-108260250	HFF-Myc	foreskin:	n/a	chr5:108260220-108260238
30	TBP	chr5:108260104-108260614	HepG2	liver:	n/a	n/a
31	CTCF	chr5:108260100-108260250	AG04450	lung:	n/a	chr5:108260220-108260238
32	CBX3	chr5:108259933-108260625	HCT-116	colon:	n/a	n/a
33	CTCF	chr5:108260100-108260250	BE2_C	brain:	n/a	chr5:108260220-108260238
34	CTCF	chr5:108260120-108260270	GM06990	blood:	n/a	chr5:108260220-108260238
35	ZNF143	chr5:108260105-108260338	K562	blood:	n/a	n/a
36	MBD4	chr5:108260001-108260619	HepG2	liver:	n/a	n/a
37	YY1	chr5:108260125-108260352	HCT-116	colon:	n/a	n/a
38	CTCF	chr5:108260120-108260270	K562	blood:	n/a	chr5:108260220-108260238
39	EP300	chr5:108260126-108260556	K562	blood:	n/a	n/a
40	MAX	chr5:108260000-108260706	HepG2	liver:	n/a	n/a
41	FOXA1	chr5:108260101-108260464	HepG2	liver:	n/a	n/a
42	HCFC1	chr5:108260117-108260475	K562	blood:	n/a	n/a
43	RAD21	chr5:108260079-108260386	HepG2	liver:	n/a	n/a
44	POLR2A	chr5:108260113-108260524	HCT-116	colon:	n/a	n/a
45	HDAC2	chr5:108260107-108260348	HepG2	liver:	n/a	n/a
46	CTCF	chr5:108260120-108260270	HMF	breast:	n/a	chr5:108260220-108260238
47	CBX3	chr5:108260085-108260391	K562	blood:	n/a	n/a
48	ELF1	chr5:108260104-108260491	HepG2	liver:	n/a	n/a
49	RAD21	chr5:108259989-108260500	HepG2	liver:	n/a	n/a
50	CTCF	chr5:108260100-108260250	HMF	breast:	n/a	chr5:108260220-108260238

Variant related genes	Relation type
FER	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11949066	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11952572	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11953198	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11953486	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11958918	0.80[EUR][1000 genomes]
rs11959681	0.89[EUR][1000 genomes]
rs11960713	0.89[EUR][1000 genomes]
rs17161573	0.93[ASN][1000 genomes]
rs17161574	0.93[ASN][1000 genomes]
rs3797817	1.00[ASN][1000 genomes]
rs3797822	1.00[ASN][1000 genomes]
rs3851456	0.93[ASN][1000 genomes]
rs56134914	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56381733	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56792678	1.00[ASN][1000 genomes]
rs57158292	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58620246	0.93[ASN][1000 genomes]
rs58642014	1.00[ASN][1000 genomes]
rs59055229	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59923567	1.00[ASN][1000 genomes]
rs61090818	1.00[ASN][1000 genomes]
rs61640970	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594344	0.80[ASN][1000 genomes]
rs66485253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66834040	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67145801	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67156774	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67338203	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6872912	0.93[ASN][1000 genomes]
rs72787096	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72787098	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72787099	0.81[AMR][1000 genomes]
rs72787100	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72787101	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72787102	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72789304	0.80[EUR][1000 genomes]
rs72789306	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72789307	0.80[EUR][1000 genomes]
rs72789308	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72789309	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72793903	0.86[EUR][1000 genomes]
rs72793905	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72793906	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72793909	0.88[EUR][1000 genomes]
rs72793918	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72793920	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72793922	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72793923	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72793926	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72793927	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72793930	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72793933	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73209329	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73209333	1.00[ASN][1000 genomes]
rs73209338	1.00[ASN][1000 genomes]
rs73209345	1.00[ASN][1000 genomes]
rs73209347	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73209352	1.00[ASN][1000 genomes]
rs73209366	1.00[ASN][1000 genomes]
rs73211525	1.00[ASN][1000 genomes]
rs73211537	1.00[ASN][1000 genomes]
rs73211547	1.00[ASN][1000 genomes]
rs73211557	1.00[ASN][1000 genomes]
rs73211567	0.93[ASN][1000 genomes]
rs73211580	0.93[ASN][1000 genomes]
rs73211584	0.80[ASN][1000 genomes]
rs73780769	1.00[ASN][1000 genomes]
rs7713828	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723264	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723604	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723612	1.00[ASN][1000 genomes]
rs7734904	0.80[EUR][1000 genomes]
rs7735425	0.80[EUR][1000 genomes]
rs7736915	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1016343	chr5:108220116-108364687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv882691	chr5:108229760-108366473	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108183800-108260400	Weak transcription	Ovary	ovary
2	chr5:108197000-108268200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:108199200-108271400	Weak transcription	Aorta	Aorta
4	chr5:108203800-108323400	Weak transcription	Primary B cells from cord blood	blood
5	chr5:108208200-108268800	Weak transcription	Primary T cells from cord blood	blood
6	chr5:108214200-108272200	Weak transcription	Gastric	stomach
7	chr5:108217600-108323200	Weak transcription	Left Ventricle	heart
8	chr5:108221400-108280600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:108229600-108269800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:108230200-108302400	Weak transcription	HSMM	muscle
11	chr5:108242200-108271000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:108244200-108295000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:108247200-108277600	Weak transcription	Fetal Lung	lung
14	chr5:108250400-108277600	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:108254000-108266400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:108254000-108269400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:108254000-108311200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:108256200-108260200	Weak transcription	GM12878-XiMat	blood
19	chr5:108259800-108260600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:108260000-108260400	Active TSS	HepG2	liver
21	chr5:108260000-108260600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:108260000-108260600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr5:108260000-108260600	Enhancers	Fetal Intestine Large	intestine
24	chr5:108260000-108260600	Enhancers	Fetal Intestine Small	intestine
25	chr5:108260000-108261000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr5:108260000-108261200	Active TSS	Dnd41	blood

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