Variant report

Variant	rs12950209
Chromosome Location	chr17:38049102-38049103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38043962..38046303-chr17:38047631..38049483,2	K562	blood:
2	chr17:38043921..38046303-chr17:38047983..38049521,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZPBP2-3	chr17:38048407-38049819	NONHSAT053490

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1008723	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011082	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1031458	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1031460	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078925	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078926	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078927	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078928	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11557466	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11557467	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11650661	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651596	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11655198	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655292	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870965	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12103884	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453507	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12603332	0.92[ASN][1000 genomes]
rs12709365	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936231	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936409	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12939832	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12946393	0.81[ASN][1000 genomes]
rs12949100	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12950743	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380815	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453559	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290400	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305479	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305480	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2872516	0.92[ASN][1000 genomes]
rs34120102	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36000226	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744246	0.82[ASN][1000 genomes]
rs4065275	0.92[ASN][1000 genomes]
rs4794820	0.90[ASN][1000 genomes]
rs4795397	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795399	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795400	0.96[ASN][1000 genomes]
rs4795401	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4795402	0.81[ASN][1000 genomes]
rs4795403	0.81[ASN][1000 genomes]
rs4795404	0.81[ASN][1000 genomes]
rs4795405	0.91[ASN][1000 genomes]
rs56380902	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62067034	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503524	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7213668	0.80[ASN][1000 genomes]
rs7216389	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7216558	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7219923	0.96[ASN][1000 genomes]
rs7221605	0.96[ASN][1000 genomes]
rs7224129	0.92[ASN][1000 genomes]
rs7224908	0.81[ASN][1000 genomes]
rs7359623	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065777	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8067378	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069176	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074437	0.94[ASN][1000 genomes]
rs8076131	0.91[ASN][1000 genomes]
rs869402	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs883770	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921649	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921650	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9303279	0.95[ASN][1000 genomes]
rs9303280	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9303281	0.96[ASN][1000 genomes]
rs9906951	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9916765	0.86[EUR][1000 genomes];0.82[ASN][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	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12950209	ORMDL3	cis	multi-tissue	Pritchard
rs12950209	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs12950209	IKZF3	cis	multi-tissue	Pritchard
rs12950209	GSDMB	cis	Whole Blood	GTEx
rs12950209	ORMDL3	cis	Whole Blood	GTEx
rs12950209	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs12950209	GSDML	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38046000-38059800	Weak transcription	Liver	Liver
2	chr17:38047400-38059200	Weak transcription	Primary T cells from cord blood	blood
3	chr17:38049000-38049200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:38049000-38050200	Weak transcription	Primary B cells from cord blood	blood

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