Variant report

Variant	rs8067378
Chromosome Location	chr17:38051348-38051349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1008723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011082	0.96[ASN][1000 genomes]
rs1031458	0.96[ASN][1000 genomes]
rs1031460	0.96[ASN][1000 genomes]
rs10445308	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[TSI][hapmap]
rs10852936	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11078925	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078926	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs11078927	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11078928	1.00[ASN][1000 genomes]
rs11557466	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11557467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11650661	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651596	0.99[ASN][1000 genomes]
rs11655198	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655292	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870965	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12103884	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453507	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12603332	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12709365	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936409	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12939832	0.99[ASN][1000 genomes]
rs12946393	0.81[ASN][1000 genomes]
rs12946510	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs12949100	1.00[ASN][1000 genomes]
rs12950209	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12950743	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380815	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453559	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305480	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs2313430	0.80[EUR][1000 genomes]
rs2872516	0.92[ASN][1000 genomes]
rs34120102	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36000226	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744246	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs3816470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs4065275	0.92[ASN][1000 genomes]
rs4794820	0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4795397	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795399	1.00[ASN][1000 genomes]
rs4795400	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4795401	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4795402	0.80[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4795403	0.80[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4795404	0.80[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4795405	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs56380902	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62067034	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503524	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7213668	0.80[ASN][1000 genomes]
rs7216389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7216558	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7219923	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7221605	0.96[ASN][1000 genomes]
rs7224129	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7224908	0.81[ASN][1000 genomes]
rs7359623	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065777	0.96[ASN][1000 genomes]
rs8069176	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs8074437	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8076131	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs869402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs883770	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907091	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs907092	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs921649	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921650	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9303277	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs9303279	0.95[ASN][1000 genomes]
rs9303280	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9303281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9635726	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs9906951	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9909593	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[TSI][hapmap]
rs9916765	0.89[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

Variant related diseases (count:2)

Disease	PMID	Source
Ulcerative colitis	20228799	GWAS catalog
Cervical cancer	23817570	GWAS catalog

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs8067378	ORMDL3	cis	lymphoblastoid	GTEx
rs8067378	ORMDL3	cis	parietal	SCAN
rs8067378	CASC3	cis	cerebellum	SCAN
rs8067378	DHRS11	cis	parietal	SCAN
rs8067378	ORMDL3	cis	lymphoblastoid	seeQTL
rs8067378	CDC6	cis	cerebellum	SCAN
rs8067378	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs8067378	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs8067378	ZNHIT3	cis	cerebellum	SCAN
rs8067378	MED24	cis	parietal	SCAN
rs8067378	IKZF3	cis	multi-tissue	Pritchard
rs8067378	GSDMB	cis	Whole Blood	GTEx
rs8067378	ORMDL3	cis	Lymphoblastoid	GTEx
rs8067378	ZPBP2	cis	lymphoblastoid	seeQTL
rs8067378	ENSG00000073605	cis	multi-tissue	Pritchard
rs8067378	GSDML	cis	multi-tissue	Pritchard
rs8067378	GSDMB	cis	multi-tissue	Pritchard
rs8067378	GSDMB	cis	cerebellum	SCAN
rs8067378	ORMDL3	cis	multi-tissue	Pritchard
rs8067378	CDK12	cis	parietal	SCAN
rs8067378	GSDMA	cis	Adipose Subcutaneous	GTEx
rs8067378	MED1	cis	cerebellum	SCAN
rs8067378	GSDMB	cis	parietal	SCAN
rs8067378	GSDMB	cis	lymphoblastoid	seeQTL
rs8067378	SEC24C	trans	cerebellum	SCAN
rs8067378	ORMDL3	cis	Whole Blood	GTEx

Chromatin state (count:19 , 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	chr17:38049200-38059800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:38049200-38075400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr17:38049800-38052600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr17:38050200-38051600	Enhancers	Primary B cells from cord blood	blood
7	chr17:38050800-38051400	Enhancers	Primary hematopoietic stem cells	blood
8	chr17:38050800-38051400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:38050800-38051400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:38050800-38051600	Enhancers	Fetal Thymus	thymus
11	chr17:38050800-38051800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr17:38050800-38052000	Enhancers	Primary B cells from peripheral blood	blood
13	chr17:38051000-38051400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr17:38051000-38051400	Enhancers	GM12878-XiMat	blood
15	chr17:38051000-38051600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:38051000-38051600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:38051000-38059000	Weak transcription	Thymus	Thymus
18	chr17:38051200-38051400	Enhancers	Duodenum Mucosa	Duodenum
19	chr17:38051200-38059400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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