Variant report

Variant	rs12936231
Chromosome Location	chr17:38029120-38029121
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38028703..38029243-chr17:38136410..38137027,2	MCF-7	breast:
2	chr17:38027253..38029353-chr17:38058744..38061451,2	K562	blood:
3	chr17:38028899..38029611-chr17:38169830..38170569,2	MCF-7	breast:
4	chr17:38027089..38030727-chr17:38135584..38137903,4	MCF-7	breast:
5	chr17:37912256..37913081-chr17:38028636..38029533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 24 )

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];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][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];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs10852936	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[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];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs11078927	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][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];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[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]
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];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[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];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[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];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[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];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[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];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];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][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];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][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];0.86[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][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]
rs8067378	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069176	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[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];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs869402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][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];0.88[GIH][hapmap];0.87[MEX][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];0.90[GIH][hapmap];0.87[MEX][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];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][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];0.81[GIH][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	esv1795575	chr17:37974075-38041762	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs12936231	GSDMA	cis	Adipose Subcutaneous	GTEx
rs12936231	CASC3	cis	cerebellum	SCAN
rs12936231	GSDMB	cis	lymphoblastoid	seeQTL
rs12936231	SNORA21	cis	parietal	SCAN
rs12936231	ZNHIT3	cis	cerebellum	SCAN
rs12936231	ORMDL3	cis	lymphoblastoid	seeQTL
rs12936231	GSDMB	cis	Whole Blood	GTEx
rs12936231	ZPBP2	cis	lymphoblastoid	seeQTL
rs12936231	MED24	cis	parietal	SCAN
rs12936231	MED1	cis	cerebellum	SCAN
rs12936231	ORMDL3	cis	lymphoblastoid	GTEx
rs12936231	SEC24C	trans	cerebellum	SCAN
rs12936231	CDK12	cis	parietal	SCAN
rs12936231	ORMDL3	cis	parietal	SCAN
rs12936231	GSDMB	cis	parietal	SCAN
rs12936231	GSDML	cis	multi-tissue	Pritchard
rs12936231	ENSG00000172057	cis	multi-tissue	Pritchard
rs12936231	DHRS11	cis	parietal	SCAN
rs12936231	ORMDL3	cis	multi-tissue	Pritchard
rs12936231	ORMDL3	cis	Lymphoblastoid	GTEx
rs12936231	GSDMB	cis	cerebellum	SCAN
rs12936231	CDC6	cis	cerebellum	SCAN
rs12936231	IKZF3	cis	multi-tissue	Pritchard
rs12936231	ORMDL3	cis	Whole Blood	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38026400-38030000	Enhancers	Primary B cells from cord blood	blood
2	chr17:38028600-38029600	Enhancers	Primary B cells from peripheral blood	blood
3	chr17:38028800-38030200	Enhancers	GM12878-XiMat	blood

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