Variant report

Variant	rs12430021
Chromosome Location	chr13:50528161-50528162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50527779..50530040-chr13:50569450..50572377,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50526411-50531031	NONHSAT033771
2	lnc-TRIM13-5	chr13:50527614-50528204	NONHSAT033773

Variant related genes	Relation type
ENSG00000264864	Chromatin interaction
ENSG00000204977	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12429041	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12429047	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12430731	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12584761	0.91[EUR][1000 genomes]
rs12585937	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1609571	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17073758	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2407879	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2897794	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4142286	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4942896	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942898	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942902	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4942903	0.91[EUR][1000 genomes]
rs7983585	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9562938	0.81[ASN][1000 genomes]
rs9562940	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9562941	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9562944	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562951	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568348	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568351	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568353	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568359	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568361	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568365	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568371	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568379	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1834429	chr13:50509784-50536186	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv1837591	chr13:50513148-50530603	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
4	nsv561630	chr13:50525141-50545402	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50511400-50537800	Weak transcription	Left Ventricle	heart
2	chr13:50513400-50532600	Weak transcription	Ovary	ovary
3	chr13:50513400-50532800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:50522400-50550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:50525000-50530000	Enhancers	Placenta	Placenta
6	chr13:50525800-50532600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr13:50526200-50530000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr13:50526600-50528600	Weak transcription	Fetal Intestine Small	intestine
9	chr13:50526600-50529000	Weak transcription	HepG2	liver
10	chr13:50527000-50528600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr13:50527800-50528200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr13:50528000-50528200	Enhancers	HSMMtube	muscle
13	chr13:50528000-50528400	Weak transcription	Fetal Intestine Large	intestine
14	chr13:50528000-50529400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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