Variant report

Variant	rs12354363
Chromosome Location	chr1:180524005-180524006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:180523701-180524067	T-47D	breast:	n/a	n/a
2	CEBPB	chr1:180523819-180524098	HepG2	liver:	n/a	chr1:180523957-180523968
3	CEBPB	chr1:180523695-180524176	MCF-7	breast:	n/a	chr1:180523957-180523968
4	CEBPB	chr1:180523793-180524111	K562	blood:	n/a	chr1:180523957-180523968
5	GATA3	chr1:180523473-180525316	MCF-7	breast:	n/a	n/a
6	CEBPB	chr1:180523833-180524102	IMR90	lung:	n/a	chr1:180523957-180523968
7	CEBPB	chr1:180523720-180524096	MCF-7	breast:	n/a	chr1:180523957-180523968
8	GATA3	chr1:180523726-180524056	T-47D	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180518213..180520300-chr1:180521624..180524471,2	K562	blood:
2	chr1:180523368..180525230-chr1:180988182..180990982,2	K562	blood:
3	chr1:180523371..180525689-chr1:180527649..180530841,3	MCF-7	breast:
4	chr1:180514007..180517933-chr1:180519953..180524083,4	K562	blood:
5	chr1:180523564..180525363-chr1:180582758..180585501,2	K562	blood:
6	chr1:180519806..180522795-chr1:180523226..180525284,2	MCF-7	breast:
7	chr1:180521347..180523149-chr1:180523872..180526102,2	K562	blood:
8	chr1:180523341..180525104-chr1:180600909..180602424,2	MCF-7	breast:
9	chr1:180520741..180525768-chr1:180529838..180532812,4	MCF-7	breast:
10	chr1:180522675..180524716-chr1:180601088..180603010,2	MCF-7	breast:
11	chr1:180520662..180524325-chr1:180527806..180530510,3	K562	blood:
12	chr1:180523696..180527243-chr1:180568963..180571816,3	MCF-7	breast:
13	chr1:180518736..180521138-chr1:180521840..180525224,3	K562	blood:

No data

No data

No data

Variant related genes	Relation type
OVAAL	TF binding region
ENSG00000143324	Chromatin interaction
ENSG00000266683	Chromatin interaction
ENSG00000236719	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10913989	1.00[AMR][1000 genomes]
rs10913993	1.00[AMR][1000 genomes]
rs10913997	1.00[AMR][1000 genomes]
rs10914015	1.00[AMR][1000 genomes]
rs10914025	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10914026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10914039	1.00[AMR][1000 genomes]
rs12060882	1.00[AMR][1000 genomes]
rs12065345	1.00[AMR][1000 genomes]
rs12065470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12068605	1.00[AMR][1000 genomes]
rs12076376	1.00[AMR][1000 genomes]
rs12078865	1.00[AMR][1000 genomes]
rs12080367	1.00[AMR][1000 genomes]
rs12080976	1.00[AMR][1000 genomes]
rs12091034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095564	1.00[AMR][1000 genomes]
rs12096761	1.00[AMR][1000 genomes]
rs12098212	1.00[AMR][1000 genomes]
rs16856167	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73051243	1.00[AMR][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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180510400-180529400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:180516600-180536800	Weak transcription	Psoas Muscle	Psoas
3	chr1:180521400-180525400	Weak transcription	Left Ventricle	heart
4	chr1:180521800-180524400	Weak transcription	K562	blood
5	chr1:180521800-180530200	Weak transcription	Right Atrium	heart
6	chr1:180523200-180525200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:180523200-180525600	Enhancers	Placenta	Placenta

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links