Variant report

Variant	rs2650000
Chromosome Location	chr12:121388962-121388963
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121388948..121393139-chr12:121395354..121400145,4	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10774579	0.84[ASN][1000 genomes]
rs11065358	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065365	0.89[ASN][1000 genomes]
rs11065385	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs1169288	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1182933	0.82[YRI][hapmap]
rs1183910	0.87[CEU][hapmap];0.84[AMR][1000 genomes]
rs1696359	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1732391	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1920792	0.92[ASN][1000 genomes]
rs2178463	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2243458	0.80[AMR][1000 genomes]
rs2244608	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2251468	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2255531	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2464190	0.87[ASN][1000 genomes]
rs2649999	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2701175	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2701194	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6489786	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7135337	0.85[ASN][1000 genomes]
rs7305618	0.91[ASN][1000 genomes]
rs7953249	0.92[ASN][1000 genomes]
rs7954039	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7954331	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1838192	chr12:121363589-121402932	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Metabolic traits	19060910	GWAS catalog
LDL cholesterol	19060906	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2650000	SPPL3	cis	cerebellum	SCAN
rs2650000	FLJ12448	cis	multi-tissue	Pritchard
rs2650000	CABP1	cis	cerebellum	SCAN
rs2650000	MLEC	cis	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121367400-121394400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:121379200-121394800	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links