Variant report

Variant	rs58557116
Chromosome Location	chr12:49682142-49682143
allele	A/G
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	ZNF143	chr12:49682117-49682628	GM12878	blood:	n/a	n/a
2	RAD21	chr12:49682111-49682498	A549	lung:	n/a	chr12:49682286-49682305
3	CTCF	chr12:49682074-49682544	K562	blood:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
4	CTCF	chr12:49682141-49682456	HUVEC	blood vessel:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
5	MAFK	chr12:49682065-49682420	Hela-S3	cervix:	n/a	chr12:49682258-49682274 chr12:49682254-49682271
6	CTCF	chr12:49682075-49682517	HepG2	liver:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
7	CTCF	chr12:49681843-49682936	A549	lung:	n/a	chr12:49682288-49682301 chr12:49682718-49682727 chr12:49682287-49682308 chr12:49682285-49682303
8	RAD21	chr12:49681975-49682766	A549	lung:	n/a	chr12:49682286-49682305
9	RAD21	chr12:49682108-49682613	HepG2	liver:	n/a	chr12:49682286-49682305
10	RAD21	chr12:49681945-49682717	HCT-116	colon:	n/a	chr12:49682286-49682305
11	JUND	chr12:49682113-49682430	HepG2	liver:	n/a	n/a
12	CREB1	chr12:49681962-49682658	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr12:49682140-49682290	HCM	heart:	n/a	n/a
14	CTCF	chr12:49682141-49682368	SK-N-SH_RA	brain:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
15	RAD21	chr12:49682062-49682665	MCF-7	breast:	n/a	chr12:49682286-49682305
16	CTCF	chr12:49682120-49682270	WI-38	lung:	n/a	n/a
17	CTCF	chr12:49682044-49682681	HCT-116	colon:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
18	MXI1	chr12:49682097-49682436	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr12:49681997-49682606	ECC-1	luminal epithelium:	n/a	chr12:49682286-49682305
20	RAD21	chr12:49681623-49682862	SK-N-SH	brain:	n/a	chr12:49682286-49682305
21	RAD21	chr12:49681964-49682602	HepG2	liver:	n/a	chr12:49682286-49682305
22	RAD21	chr12:49681927-49682719	MCF-7	breast:	n/a	chr12:49682286-49682305
23	RAD21	chr12:49682027-49682608	A549	lung:	n/a	chr12:49682286-49682305
24	USF2	chr12:49681935-49682374	GM12878	blood:	n/a	n/a
25	CTCF	chr12:49682070-49682550	GM12878	blood:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
26	BRCA1	chr12:49682098-49682409	GM12878	blood:	n/a	n/a
27	CTCF	chr12:49682075-49682512	IMR90	lung:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
28	CTCF	chr12:49682055-49682545	A549	lung:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
29	CTCF	chr12:49682019-49682555	A549	lung:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
30	JUND	chr12:49682127-49682435	H1-hESC	embryonic stem cell:	n/a	n/a
31	RAD21	chr12:49681985-49682617	H1-hESC	embryonic stem cell:	n/a	chr12:49682286-49682305
32	SMC3	chr12:49681775-49683027	SK-N-SH	brain:	n/a	chr12:49682882-49682890 chr12:49682287-49682301
33	CREB1	chr12:49682053-49682664	HepG2	liver:	n/a	n/a
34	CTCF	chr12:49682135-49682480	K562	blood:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
35	ATF2	chr12:49682026-49682523	H1-hESC	embryonic stem cell:	n/a	n/a
36	JUND	chr12:49682135-49682487	K562	blood:	n/a	n/a
37	EP300	chr12:49682117-49682473	K562	blood:	n/a	chr12:49682163-49682177
38	SMC3	chr12:49682084-49682759	Hela-S3	cervix:	n/a	chr12:49682287-49682301
39	CTCF	chr12:49681906-49682880	HCT-116	colon:	n/a	chr12:49682288-49682301 chr12:49682718-49682727 chr12:49682287-49682308 chr12:49682285-49682303
40	SMC3	chr12:49682089-49682530	K562	blood:	n/a	chr12:49682287-49682301
41	CREB1	chr12:49682033-49682532	HepG2	liver:	n/a	n/a
42	CTCF	chr12:49682137-49682448	GM12878	blood:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
43	CTCF	chr12:49682115-49682477	T-47D	breast:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
44	RAD21	chr12:49682083-49682505	GM12878	blood:	n/a	chr12:49682286-49682305
45	RAD21	chr12:49682085-49682561	H1-hESC	embryonic stem cell:	n/a	chr12:49682286-49682305
46	CTCF	chr12:49682064-49682585	MCF-7	breast:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
47	ZNF263	chr12:49681852-49683145	HEK293-T-REx	kidney:	n/a	n/a
48	RAD21	chr12:49682100-49682487	K562	blood:	n/a	chr12:49682286-49682305
49	ATF1	chr12:49682086-49682445	K562	blood:	n/a	n/a
50	MAZ	chr12:49682121-49682457	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49681725..49683047-chr12:49690017..49691263,7	K562	blood:
2	chr12:49681949..49682809-chr12:49742499..49743052,2	K562	blood:
3	chr12:49681842..49683325-chr12:49740711..49741813,10	K562	blood:
4	chr12:49581641..49584379-chr12:49680689..49682648,2	MCF-7	breast:
5	chr12:49674656..49677388-chr12:49681241..49683027,2	K562	blood:
6	chr12:49681831..49682839-chr12:49735834..49736883,5	MCF-7	breast:
7	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
8	chr12:49681907..49682823-chr12:49741104..49742122,6	MCF-7	breast:
9	chr12:49682057..49682830-chr12:49690034..49691299,9	MCF-7	breast:
10	chr12:49680157..49683584-chr12:49686626..49689914,4	K562	blood:
11	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
12	chr12:49681831..49682779-chr12:49752157..49753107,3	MCF-7	breast:
13	chr12:49681953..49682967-chr12:49730581..49731487,4	K562	blood:
14	chr12:49681895..49684314-chr12:49959799..49961402,2	MCF-7	breast:
15	chr12:49670426..49673698-chr12:49680662..49684493,5	K562	blood:
16	chr12:49657412..49661097-chr12:49680173..49683104,4	MCF-7	breast:
17	chr12:49667402..49669417-chr12:49680548..49682820,2	K562	blood:
18	chr12:49681373..49684532-chr12:49689640..49692033,4	MCF-7	breast:
19	chr12:49677107..49685653-chr12:49686694..49692276,10	MCF-7	breast:
20	chr12:49681839..49682839-chr12:49731008..49731599,2	MCF-7	breast:
21	chr12:49681812..49682734-chr12:49750562..49751558,2	K562	blood:
22	chr12:49682050..49682799-chr3:140769790..140770351,2	MCF-7	breast:
23	chr12:49677467..49679581-chr12:49679946..49682245,2	K562	blood:
24	chr12:49681072..49683982-chr12:49740042..49742120,4	MCF-7	breast:
25	chr12:49681807..49682815-chr12:49750578..49751528,4	MCF-7	breast:
26	chr12:49681784..49683022-chr12:49735866..49736958,14	K562	blood:
27	chr12:49681835..49682776-chr12:49735729..49737096,6	MCF-7	breast:
28	chr12:49665631..49676200-chr12:49678297..49684493,17	K562	blood:
29	chr12:49682080..49684336-chr12:49718249..49720945,2	MCF-7	breast:
30	chr12:49678740..49680286-chr12:49680841..49682374,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1QL4-2	chr12:49681292-49682146	XLOC_010069
2	lnc-C1QL4-1	chr12:49681827-49682146	NONHSAT028097
3	lnc-C1QL4-1	chr12:49679532-49682146	NONHSAT028095

Variant related genes	Relation type
PRPH	TF binding region
ENSG00000135451	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000175093	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258334	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11830820	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11836976	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17853062	1.00[AMR][1000 genomes]
rs56005192	1.00[AMR][1000 genomes]
rs56014465	1.00[AMR][1000 genomes]
rs56140046	1.00[AMR][1000 genomes]
rs56330550	1.00[AMR][1000 genomes]
rs59493874	1.00[AMR][1000 genomes]
rs60712360	1.00[AMR][1000 genomes]
rs60865902	1.00[AMR][1000 genomes]
rs61110708	1.00[AMR][1000 genomes]
rs7296117	1.00[AMR][1000 genomes]
rs7299056	1.00[AMR][1000 genomes]
rs7309243	1.00[AMR][1000 genomes]
rs74089008	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74089010	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089028	1.00[AMR][1000 genomes]
rs74089030	1.00[AMR][1000 genomes]
rs74089031	1.00[AMR][1000 genomes]
rs74089060	1.00[AMR][1000 genomes]
rs74091029	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	esv19135	chr12:49676002-49690399	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv558834	chr12:49676010-49691567	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49668600-49682400	Weak transcription	HMEC	breast
2	chr12:49678200-49686800	Weak transcription	HSMM	muscle
3	chr12:49681600-49682200	Enhancers	HSMMtube	muscle
4	chr12:49681800-49682200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:49682000-49682800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:49682000-49683200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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