Variant report

Variant	rs74089008
Chromosome Location	chr12:49682599-49682600
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	CTCF	chr12:49681843-49682936	A549	lung:	n/a	chr12:49682288-49682301 chr12:49682718-49682727 chr12:49682287-49682308 chr12:49682285-49682303
3	RAD21	chr12:49681975-49682766	A549	lung:	n/a	chr12:49682286-49682305
4	RAD21	chr12:49682108-49682613	HepG2	liver:	n/a	chr12:49682286-49682305
5	RAD21	chr12:49681945-49682717	HCT-116	colon:	n/a	chr12:49682286-49682305
6	CREB1	chr12:49681962-49682658	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr12:49682460-49682610	GM12864	blood:	n/a	n/a
8	ZMIZ1	chr12:49682220-49682612	K562	blood:	n/a	n/a
9	RAD21	chr12:49682062-49682665	MCF-7	breast:	n/a	chr12:49682286-49682305
10	CTCF	chr12:49682044-49682681	HCT-116	colon:	n/a	chr12:49682288-49682301 chr12:49682287-49682308 chr12:49682285-49682303
11	RAD21	chr12:49681997-49682606	ECC-1	luminal epithelium:	n/a	chr12:49682286-49682305
12	RAD21	chr12:49681623-49682862	SK-N-SH	brain:	n/a	chr12:49682286-49682305
13	RAD21	chr12:49681964-49682602	HepG2	liver:	n/a	chr12:49682286-49682305
14	RAD21	chr12:49681927-49682719	MCF-7	breast:	n/a	chr12:49682286-49682305
15	RAD21	chr12:49682027-49682608	A549	lung:	n/a	chr12:49682286-49682305
16	RAD21	chr12:49681985-49682617	H1-hESC	embryonic stem cell:	n/a	chr12:49682286-49682305
17	SMC3	chr12:49681775-49683027	SK-N-SH	brain:	n/a	chr12:49682882-49682890 chr12:49682287-49682301
18	CREB1	chr12:49682053-49682664	HepG2	liver:	n/a	n/a
19	SMC3	chr12:49682084-49682759	Hela-S3	cervix:	n/a	chr12:49682287-49682301
20	CTCF	chr12:49681906-49682880	HCT-116	colon:	n/a	chr12:49682288-49682301 chr12:49682718-49682727 chr12:49682287-49682308 chr12:49682285-49682303
21	RCOR1	chr12:49682264-49682705	K562	blood:	n/a	n/a
22	ZNF263	chr12:49681852-49683145	HEK293-T-REx	kidney:	n/a	n/a
23	CTCF	chr12:49681455-49682909	SK-N-SH	brain:	n/a	chr12:49682288-49682301 chr12:49682718-49682727 chr12:49682287-49682308 chr12:49682285-49682303
24	CTCF	chr12:49682480-49682630	BJ	skin:	n/a	n/a
25	RAD21	chr12:49681974-49682723	ECC-1	luminal epithelium:	n/a	chr12:49682286-49682305
26	ZNF143	chr12:49682169-49682672	K562	blood:	n/a	n/a
27	KAP1	chr12:49682148-49682719	U2OS	brain:	n/a	n/a
28	STAT1	chr12:49682141-49682706	GM12878	blood:	n/a	n/a
29	ZNF143	chr12:49682132-49682713	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZNF143	chr12:49682204-49682630	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr12:49682580-49682730	HBMEC	blood vessel:	n/a	chr12:49682718-49682727
32	CTCF	chr12:49682590-49682652	GM12878	blood:	n/a	n/a
33	RCOR1	chr12:49682112-49682668	K562	blood:	n/a	n/a
34	RAD21	chr12:49682085-49682661	Hela-S3	cervix:	n/a	chr12:49682286-49682305
35	RAD21	chr12:49681956-49682754	HCT-116	colon:	n/a	chr12:49682286-49682305
36	CTCF	chr12:49682521-49682644	HUVEC	blood vessel:	n/a	n/a
37	RCOR1	chr12:49682205-49682665	Hela-S3	cervix:	n/a	n/a
38	RAD21	chr12:49682106-49682628	IMR90	lung:	n/a	chr12:49682286-49682305
39	MAFK	chr12:49682116-49682695	K562	blood:	n/a	chr12:49682258-49682274 chr12:49682254-49682271

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	chr12:49674974..49678602-chr12:49682204..49684622,3	MCF-7	breast:
4	chr12:49681842..49683325-chr12:49740711..49741813,10	K562	blood:
5	chr12:49581641..49584379-chr12:49680689..49682648,2	MCF-7	breast:
6	chr12:49674656..49677388-chr12:49681241..49683027,2	K562	blood:
7	chr12:49681831..49682839-chr12:49735834..49736883,5	MCF-7	breast:
8	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
9	chr12:49681907..49682823-chr12:49741104..49742122,6	MCF-7	breast:
10	chr12:49682057..49682830-chr12:49690034..49691299,9	MCF-7	breast:
11	chr12:49680157..49683584-chr12:49686626..49689914,4	K562	blood:
12	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
13	chr12:49681831..49682779-chr12:49752157..49753107,3	MCF-7	breast:
14	chr12:49681953..49682967-chr12:49730581..49731487,4	K562	blood:
15	chr12:49681895..49684314-chr12:49959799..49961402,2	MCF-7	breast:
16	chr12:49670426..49673698-chr12:49680662..49684493,5	K562	blood:
17	chr12:49657412..49661097-chr12:49680173..49683104,4	MCF-7	breast:
18	chr12:49667402..49669417-chr12:49680548..49682820,2	K562	blood:
19	chr12:49681373..49684532-chr12:49689640..49692033,4	MCF-7	breast:
20	chr12:49677107..49685653-chr12:49686694..49692276,10	MCF-7	breast:
21	chr12:49681839..49682839-chr12:49731008..49731599,2	MCF-7	breast:
22	chr12:49681812..49682734-chr12:49750562..49751558,2	K562	blood:
23	chr12:49682050..49682799-chr3:140769790..140770351,2	MCF-7	breast:
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	chr12:49656722..49663896-chr12:49682381..49687774,8	K562	blood:
28	chr12:49681835..49682776-chr12:49735729..49737096,6	MCF-7	breast:
29	chr12:49665631..49676200-chr12:49678297..49684493,17	K562	blood:
30	chr12:49682080..49684336-chr12:49718249..49720945,2	MCF-7	breast:
31	chr12:49668368..49669871-chr12:49682424..49685316,2	MCF-7	breast:

Variant related genes	Relation type
PRPH	TF binding region
ENSG00000175093	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000178401	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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11836976	0.91[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]
rs58557116	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59493874	1.00[AMR][1000 genomes]
rs60712360	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60865902	1.00[AMR][1000 genomes]
rs61110708	1.00[AMR][1000 genomes]
rs7296117	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7299056	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7309243	1.00[AMR][1000 genomes]
rs74089010	0.91[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	0.81[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:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49678200-49686800	Weak transcription	HSMM	muscle
2	chr12:49682000-49682800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:49682000-49683200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:49682200-49682800	Enhancers	Dnd41	blood
5	chr12:49682200-49686800	Weak transcription	HSMMtube	muscle
6	chr12:49682400-49682600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
7	chr12:49682400-49682600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
8	chr12:49682400-49682600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:49682400-49682600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
10	chr12:49682400-49682600	Bivalent Enhancer	Fetal Intestine Large	intestine
11	chr12:49682400-49682600	Flanking Active TSS	Fetal Kidney	kidney
12	chr12:49682400-49682800	Enhancers	Hela-S3	cervix
13	chr12:49682400-49683200	Enhancers	NHEK	skin
14	chr12:49682400-49683400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:49682400-49683400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:49682400-49683400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:49682400-49683400	Enhancers	HMEC	breast

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