Variant report

Variant	rs9909593
Chromosome Location	chr17:37970149-37970150
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	chr17:37924784..37926375-chr17:37969681..37972585,2	MCF-7	breast:
2	chr17:37964384..37967341-chr17:37969049..37971628,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1008723	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs10445308	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10852936	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs11078921	0.80[JPT][hapmap]
rs11078925	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs11078926	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap]
rs11078927	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.96[MEX][hapmap]
rs11557466	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[EUR][1000 genomes]
rs11557467	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap]
rs11658993	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11870965	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs12603332	0.90[CHB][hapmap]
rs12936231	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs12942330	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12944882	0.85[ASN][1000 genomes]
rs12946510	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290400	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs2305479	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap]
rs2305480	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2313430	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2941522	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2952140	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2952144	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816470	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs4794820	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4795395	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795397	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4795400	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4795405	0.82[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.96[MEX][hapmap]
rs7216389	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs7219923	0.85[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs7224129	0.85[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs8069176	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs8076131	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.91[MEX][hapmap]
rs869402	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs907091	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs907092	0.96[CEU][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9303277	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303280	0.94[CHB][hapmap]
rs9303281	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs9635726	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9747973	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs9909593	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs9909593	CDC6	cis	cerebellum	SCAN
rs9909593	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs9909593	ORMDL3	cis	multi-tissue	Pritchard
rs9909593	ORMDL3	cis	lymphoblastoid	seeQTL
rs9909593	PIGW	cis	parietal	SCAN
rs9909593	MED24	cis	parietal	SCAN
rs9909593	MED24	cis	cerebellum	SCAN
rs9909593	ZNHIT3	cis	cerebellum	SCAN
rs9909593	ORMDL3	cis	Whole Blood	GTEx
rs9909593	MED1	cis	cerebellum	SCAN
rs9909593	GSDMB	cis	Whole Blood	GTEx
rs9909593	ORMDL3	cis	parietal	SCAN
rs9909593	GSDMB	cis	cerebellum	SCAN
rs9909593	ORMDL3	cis	lymphoblastoid	GTEx
rs9909593	PGAP3	cis	Thyroid	GTEx
rs9909593	IKZF3	cis	multi-tissue	Pritchard
rs9909593	DHRS11	cis	parietal	SCAN
rs9909593	CDK12	cis	parietal	SCAN
rs9909593	GSDMA	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37966800-37974000	Strong transcription	GM12878-XiMat	blood
2	chr17:37968200-37971400	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr17:37968800-37970600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:37968800-37971000	Enhancers	Dnd41	blood
5	chr17:37969000-37970800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:37969600-37970200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:37969600-37970400	Genic enhancers	Primary B cells from cord blood	blood
8	chr17:37969600-37970400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr17:37969600-37970400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr17:37969600-37970400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr17:37969600-37970400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr17:37969600-37970600	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr17:37969600-37970600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr17:37969600-37970800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr17:37969600-37970800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr17:37969800-37970200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr17:37969800-37970400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr17:37969800-37970400	Flanking Active TSS	Thymus	Thymus
19	chr17:37969800-37970600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr17:37969800-37970600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr17:37970000-37970200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr17:37970000-37970200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:37970000-37970200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr17:37970000-37970200	Enhancers	Fetal Lung	lung
25	chr17:37970000-37970400	Flanking Active TSS	Fetal Thymus	thymus

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