Variant report

Variant	rs3816470
Chromosome Location	chr17:37985801-37985802
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	chr17:37980608..37984471-chr17:37984850..37987192,3	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1008723	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10445308	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs10852936	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11078925	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11078926	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs11078927	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs11557466	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11557467	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11870965	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12603332	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12936231	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]
rs12944882	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12946510	0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[MEX][hapmap]
rs1453559	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2290400	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2305479	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs2305480	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2313430	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2941522	0.86[EUR][1000 genomes]
rs2952140	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2952144	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3744246	0.88[JPT][hapmap]
rs4794820	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs4795395	0.84[ASN][1000 genomes]
rs4795397	0.82[CEU][hapmap];0.84[ASN][1000 genomes]
rs4795400	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs4795402	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs4795403	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs4795404	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs4795405	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs7216389	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs7219923	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7224129	0.96[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap]
rs8069176	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs8076131	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs869402	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs907091	0.88[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs907092	0.94[CHD][hapmap];0.84[MEX][hapmap]
rs9303277	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9303280	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9303281	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs9635726	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs9747973	0.87[EUR][1000 genomes]
rs9909593	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]
rs9916765	0.84[AMR][1000 genomes];0.89[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
rs3816470	GSDML	cis	multi-tissue	Pritchard
rs3816470	ZNHIT3	cis	cerebellum	SCAN
rs3816470	GSDMB	cis	Whole Blood	GTEx
rs3816470	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs3816470	PIGW	cis	parietal	SCAN
rs3816470	IKZF3	cis	multi-tissue	Pritchard
rs3816470	ORMDL3	cis	parietal	SCAN
rs3816470	MED24	cis	parietal	SCAN
rs3816470	MED1	cis	cerebellum	SCAN
rs3816470	ORMDL3	cis	Lymphoblastoid	GTEx
rs3816470	GSDMB	cis	parietal	SCAN
rs3816470	GSDMB	cis	cerebellum	SCAN
rs3816470	CDC6	cis	cerebellum	SCAN
rs3816470	ORMDL3	cis	lymphoblastoid	seeQTL
rs3816470	CDK12	cis	parietal	SCAN
rs3816470	ORMDL3	cis	multi-tissue	Pritchard
rs3816470	GSDMB	cis	lymphoblastoid	seeQTL
rs3816470	ORMDL3	cis	lymphoblastoid	GTEx
rs3816470	SNORA21	cis	parietal	SCAN
rs3816470	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs3816470	ORMDL3	cis	Whole Blood	GTEx
rs3816470	GSDMA	cis	Adipose Subcutaneous	GTEx
rs3816470	DHRS11	cis	parietal	SCAN
rs3816470	CCR7	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37979400-37986600	ZNF genes & repeats	GM12878-XiMat	blood
2	chr17:37979400-37991800	Weak transcription	Gastric	stomach
3	chr17:37980200-37986600	Strong transcription	Primary T cells from cord blood	blood
4	chr17:37980600-37986400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:37980600-37986600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:37981000-37987200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr17:37981000-37987400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:37981400-37987200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:37981600-37988600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:37981800-37986600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
11	chr17:37981800-37988000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr17:37982000-37987600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr17:37982400-37991000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr17:37982600-37993800	Strong transcription	Primary B cells from cord blood	blood
15	chr17:37984400-37993400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr17:37985000-37990400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:37985000-37991200	Weak transcription	Spleen	Spleen
18	chr17:37985000-37994800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr17:37985000-37996200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr17:37985400-37991200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:37985600-37997800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr17:37985800-37987200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr17:37985800-37990800	Weak transcription	Fetal Thymus	thymus
24	chr17:37985800-37991600	Weak transcription	Thymus	Thymus
25	chr17:37985800-37994800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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