Variant report

Variant	rs12080483
Chromosome Location	chr1:159768619-159768620
allele	G/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	RAD21	chr1:159768525-159769174	A549	lung:	n/a	chr1:159768780-159768799
2	RAD21	chr1:159768531-159769072	MCF-7	breast:	n/a	chr1:159768780-159768799
3	RAD21	chr1:159768584-159769118	Hela-S3	cervix:	n/a	chr1:159768780-159768799
4	CTCF	chr1:159768331-159769406	HCT-116	colon:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
5	MAX	chr1:159768526-159769174	A549	lung:	n/a	n/a
6	CTCF	chr1:159768506-159769213	MCF-7	breast:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
7	RAD21	chr1:159768579-159769067	SK-N-SH_RA	brain:	n/a	chr1:159768780-159768799
8	ZC3H11A	chr1:159768573-159768967	K562	blood:	n/a	n/a
9	WRNIP1	chr1:159768541-159769349	GM12878	blood:	n/a	n/a
10	RAD21	chr1:159768423-159769414	SK-N-SH	brain:	n/a	chr1:159768780-159768799
11	YY1	chr1:159768562-159769128	H1-hESC	embryonic stem cell:	n/a	chr1:159768830-159768849
12	RAD21	chr1:159768608-159769038	GM12878	blood:	n/a	chr1:159768780-159768799
13	RAD21	chr1:159768509-159769122	IMR90	lung:	n/a	chr1:159768780-159768799
14	CBX3	chr1:159768487-159769320	HCT-116	colon:	n/a	n/a
15	RAD21	chr1:159768563-159769118	H1-hESC	embryonic stem cell:	n/a	chr1:159768780-159768799
16	RAD21	chr1:159768551-159769089	MCF-7	breast:	n/a	chr1:159768780-159768799
17	CTCF	chr1:159768604-159769062	ECC-1	luminal epithelium:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
18	RAD21	chr1:159768546-159769111	SK-N-SH_RA	brain:	n/a	chr1:159768780-159768799
19	ZNF143	chr1:159768602-159768990	GM12878	blood:	n/a	n/a
20	CTCF	chr1:159768509-159769188	A549	lung:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
21	CTCF	chr1:159768571-159769017	T-47D	breast:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
22	CTCF	chr1:159768594-159769034	K562	blood:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
23	RAD21	chr1:159768598-159769128	H1-hESC	embryonic stem cell:	n/a	chr1:159768780-159768799
24	CTCF	chr1:159768582-159768974	A549	lung:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
25	ZNF143	chr1:159768610-159769019	K562	blood:	n/a	n/a
26	CTCF	chr1:159768607-159769027	HepG2	liver:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
27	RAD21	chr1:159768597-159768981	HepG2	liver:	n/a	chr1:159768780-159768799
28	RAD21	chr1:159768616-159769005	HepG2	liver:	n/a	chr1:159768780-159768799
29	CTCF	chr1:159768550-159769094	A549	lung:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
30	RAD21	chr1:159768528-159769086	H1-hESC	embryonic stem cell:	n/a	chr1:159768780-159768799
31	RFX5	chr1:159768616-159768960	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr1:159768601-159769012	K562	blood:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
33	SMC3	chr1:159768587-159769109	Hela-S3	cervix:	n/a	chr1:159768781-159768795
34	CTCF	chr1:159768567-159769119	IMR90	lung:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
35	CTCF	chr1:159768580-159768730	HAc	cerebellar:	n/a	n/a
36	CTCF	chr1:159768395-159769219	HCT-116	colon:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
37	SMC3	chr1:159768616-159769140	K562	blood:	n/a	chr1:159768781-159768795
38	MYC	chr1:159768614-159769037	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr1:159768580-159769062	H1-hESC	embryonic stem cell:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
40	MYC	chr1:159768564-159769026	MCF10A-Er-Src	breast:	n/a	n/a
41	CTCF	chr1:159768601-159769002	Spleen_OC	spleen:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
42	EBF1	chr1:159768578-159768965	GM12878	blood:	n/a	n/a
43	CTCF	chr1:159768578-159769098	K562	blood:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
44	E2F4	chr1:159768611-159769011	MCF10A-Er-Src	breast:	n/a	n/a
45	RAD21	chr1:159768358-159769319	HCT-116	colon:	n/a	chr1:159768780-159768799
46	RAD21	chr1:159768549-159769211	ECC-1	luminal epithelium:	n/a	chr1:159768780-159768799
47	RAD21	chr1:159768407-159769270	HCT-116	colon:	n/a	chr1:159768780-159768799
48	RAD21	chr1:159768537-159769142	ECC-1	luminal epithelium:	n/a	chr1:159768780-159768799
49	CTCF	chr1:159768601-159769005	A549	lung:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
50	RAD21	chr1:159768594-159768989	HepG2	liver:	n/a	chr1:159768780-159768799

No.	Distal block	Cell Line	Cell type
1	chr1:159767764..159770005-chr1:159860953..159862581,56	MCF-7	breast:
2	chr1:159767618..159769808-chr1:159861062..159862249,21	MCF-7	breast:
3	chr1:159768345..159769282-chr1:159859526..159860741,4	MCF-7	breast:
4	chr1:159768315..159769250-chr1:159861096..159861662,3	K562	blood:
5	chr1:159767829..159770101-chr1:159851843..159854552,2	MCF-7	breast:
6	chr1:159768046..159769566-chr1:159975811..159977855,12	K562	blood:
7	chr1:159768235..159769330-chr1:159915062..159916235,4	K562	blood:
8	chr1:159768310..159769697-chr1:159798745..159799727,11	MCF-7	breast:
9	chr1:159767920..159768832-chr1:159977164..159978145,2	MCF-7	breast:
10	chr1:159767187..159770392-chr1:159770720..159774821,3	K562	blood:
11	chr1:159760951..159764398-chr1:159766034..159769710,4	K562	blood:
12	chr1:159766964..159768687-chr1:159770720..159772880,2	K562	blood:

Variant related genes	Relation type
FCRL6	TF binding region
ENSG00000181036	Chromatin interaction
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12061921	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12083595	1.00[CEU][hapmap]
rs12092214	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12092557	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3935782	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4076130	0.92[EUR][1000 genomes]
rs61689224	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73028938	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv521503	chr1:159762120-159795478	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159765600-159770000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:159768400-159771400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:159768600-159770200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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