Variant report

Variant	rs662889
Chromosome Location	chr12:123188079-123188080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr12:123187789-123188123	HepG2	liver:	n/a	n/a
2	FOXA1	chr12:123187806-123188302	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:123187655-123188092	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr12:123187750-123188250	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr12:123187528-123188305	MCF10A-Er-Src	breast:	n/a	chr12:123187645-123187666
6	FOS	chr12:123187706-123188305	MCF10A-Er-Src	breast:	n/a	n/a
7	EBF1	chr12:123187949-123188264	GM12878	blood:	n/a	n/a
8	POU2F2	chr12:123188001-123188214	GM12878	blood:	n/a	n/a
9	FOS	chr12:123187821-123188180	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr12:123187570-123188311	MCF10A-Er-Src	breast:	n/a	n/a
11	E2F4	chr12:123187896-123188134	MCF10A-Er-Src	breast:	n/a	n/a
12	FOXA1	chr12:123187829-123188220	HepG2	liver:	n/a	n/a
13	EBF1	chr12:123187913-123188259	GM12878	blood:	n/a	n/a
14	POU2F2	chr12:123187839-123188275	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:123187462-123188263	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr12:123187510-123188458	MCF10A-Er-Src	breast:	n/a	chr12:123187645-123187666
17	FOXA2	chr12:123187936-123188118	HepG2	liver:	n/a	n/a
18	STAT3	chr12:123187886-123188097	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr12:123187833-123188233	Hela-S3	cervix:	n/a	n/a
20	MYC	chr12:123187728-123188305	MCF10A-Er-Src	breast:	n/a	n/a
21	CEBPB	chr12:123187794-123188089	HepG2	liver:	n/a	n/a
22	FOS	chr12:123187796-123188158	MCF10A-Er-Src	breast:	n/a	n/a
23	STAT3	chr12:123187514-123188307	MCF10A-Er-Src	breast:	n/a	chr12:123187645-123187666
24	CEBPB	chr12:123187869-123188146	A549	lung:	n/a	n/a
25	STAT3	chr12:123187750-123188301	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:123188078-123188128	HepG2	liver:	n/a
2	chr12:123188078-123188128	SKMC	muscle:	n/a
3	chr12:123188078-123188128	H1-hESC	embryonic stem cell:	embryo
4	chr12:123188078-123188128	AoSMC	blood vessel:	n/a
5	chr12:123188078-123188128	HCM	heart:	n/a
6	chr12:123188078-123188128	HEEpiC	esophagus:	n/a
7	chr12:123188078-123188128	HMEC	breast:	n/a
8	chr12:123188078-123188128	HEK293	kidney:	embryo
9	chr12:123188078-123188128	NT2-D1	testis:	n/a
10	chr12:123188078-123188128	CMK	blood:	n/a
11	chr12:123188078-123188128	GM06990	blood:	n/a
12	chr12:123188078-123188128	LNCaP	prostate:	n/a
13	chr12:123188078-123188128	HL-60	blood:	n/a
14	chr12:123188078-123188128	SK-N-SH	brain:	n/a
15	chr12:123188078-123188128	BE2_C	brain:	n/a
16	chr12:123188078-123188128	HRE	kidney:	n/a
17	chr12:123188078-123188128	SAEC	small airway:	n/a
18	chr12:123188078-123188128	GM12878	blood:	n/a
19	chr12:123188078-123188128	Jurkat	blood:	n/a
20	chr12:123188078-123188128	NHDF-neo	bronchial:	n/a
21	chr12:123188078-123188128	Caco-2	colon:	n/a
22	chr12:123188078-123188128	GM12892	blood:	n/a
23	chr12:123188078-123188128	ovcar-3	ovarian:	n/a
24	chr12:123188078-123188128	U87	brain:	n/a
25	chr12:123188078-123188128	NH-A	brain:	n/a
26	chr12:123188078-123188128	PANC-1	pancreas:	n/a
27	chr12:123188078-123188128	HCF	heart:	n/a
28	chr12:123188078-123188128	ECC-1	luminal epithelium:	n/a
29	chr12:123188078-123188128	K562	blood:	n/a
30	chr12:123188078-123188128	PFSK-1	brain:	n/a
31	chr12:123188078-123188128	ProgFib	skin:	n/a
32	chr12:123188078-123188128	NB4	blood:	n/a
33	chr12:123188078-123188128	AG04449	skin:	fetal
34	chr12:123188078-123188128	Hela-S3	cervix:	n/a
35	chr12:123188078-123188128	AG04450	lung:	fetal
36	chr12:123188078-123188128	HCT-116	colon:	n/a
37	chr12:123188078-123188128	MCF-7	breast:	n/a
38	chr12:123188078-123188128	A549	lung:	n/a
39	chr12:123188078-123188128	HAEpiC	amniotic membrane:	n/a
40	chr12:123188078-123188128	NHBE	bronchial:	n/a
41	chr12:123188078-123188128	SK-N-MC	brain:	n/a
42	chr12:123188078-123188128	IMR90	lung:	fetal
43	chr12:123188078-123188128	AG09309	skin:	n/a
44	chr12:123188078-123188128	HRPEpiC	eye:	n/a
45	chr12:123188078-123188128	HIPEpiC	eye:	n/a
46	chr12:123188078-123188128	MCF10A-Er-Src	breast:	n/a
47	chr12:123188078-123188128	GM12891	blood:	n/a
48	chr12:123188078-123188128	HPAEpiC	pulmonary alveolar:	n/a
49	chr12:123188078-123188128	HRCEpiC	kidney:	n/a
50	chr12:123188078-123188128	Hepatocyte	liver:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123186486..123188573-chr12:123199930..123201817,2	MCF-7	breast:

No data

Variant related genes	Relation type
HCAR2	TF binding region
HCAR2	CpG island
ENSG00000255398	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11059384	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1696336	0.84[AMR][1000 genomes]
rs1798218	0.91[AMR][1000 genomes]
rs1798219	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2244689	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2262194	0.86[ASN][1000 genomes]
rs2454702	0.84[ASN][1000 genomes]
rs2454722	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2649991	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3104613	0.83[ASN][1000 genomes]
rs3104614	0.83[ASN][1000 genomes]
rs34699072	0.85[ASN][1000 genomes]
rs35683065	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3922628	0.84[ASN][1000 genomes]
rs4759361	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4759364	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4759404	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs488635	0.85[ASN][1000 genomes]
rs491489	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492699	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs507525	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs509548	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs525215	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526276	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs537527	0.85[ASN][1000 genomes]
rs545234	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562042	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs568853	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs580063	0.82[ASN][1000 genomes]
rs582452	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs582856	0.84[AMR][1000 genomes]
rs585465	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs589154	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs601339	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs630408	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs632393	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs635400	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs643285	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs645491	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6489203	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71456771	0.85[ASN][1000 genomes]
rs7296217	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7956284	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7969523	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13329	chr12:123178106-123210671	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	esv3379602	chr12:123179885-123191721	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	esv3336946	chr12:123180291-123193845	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	esv8843	chr12:123181591-123195219	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
5	nsv973132	chr12:123184783-123201537	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
6	esv3500953	chr12:123184899-123189597	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	esv3500964	chr12:123184899-123189597	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	esv3486411	chr12:123186029-123195050	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
9	esv3486412	chr12:123186029-123195050	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
10	esv8582	chr12:123186451-123200127	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
11	esv3504363	chr12:123186465-123200093	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
12	esv3504374	chr12:123186465-123200093	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv3493297	chr12:123187437-123200966	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	esv3493308	chr12:123187437-123200966	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123174000-123199800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:123184000-123188800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:123185400-123188200	Active TSS	Primary B cells from cord blood	blood
4	chr12:123186000-123188200	Enhancers	NHEK	skin
5	chr12:123186000-123188600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:123186000-123188600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:123187400-123188200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:123187400-123188600	Enhancers	Hela-S3	cervix
9	chr12:123187600-123188200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:123187600-123188200	Enhancers	HepG2	liver
11	chr12:123187800-123198600	Weak transcription	Adipose Nuclei	Adipose
12	chr12:123188000-123193600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links