Variant report

Variant	rs907092
Chromosome Location	chr17:37922259-37922260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF274	chr17:37921941-37922454	NT2-D1	testis:	n/a	n/a
2	POLR2A	chr17:37922005-37922403	GM12891	blood:	n/a	n/a
3	POLR2A	chr17:37921964-37923301	GM12892	blood:	n/a	n/a
4	POLR2A	chr17:37921826-37923949	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:37922010-37922689	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:37921968-37922374	GM12892	blood:	n/a	n/a
7	POLR2A	chr17:37922211-37923095	GM12892	blood:	n/a	n/a
8	POLR2A	chr17:37920428-37924037	GM12891	blood:	n/a	n/a
9	MAFK	chr17:37922256-37922521	HepG2	liver:	n/a	chr17:37922360-37922375
10	POLR2A	chr17:37922002-37922698	GM12878	blood:	n/a	n/a
11	POLR2A	chr17:37921968-37923880	GM12878	blood:	n/a	n/a
12	POLR2A	chr17:37920702-37923877	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37921292..37924332-chr17:37924754..37927862,3	MCF-7	breast:
2	chr17:37779913..37781548-chr17:37921179..37923723,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264198	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1008723	0.82[CEU][hapmap];0.89[CHD][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10445308	0.81[ASW][hapmap];0.96[CEU][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10852936	0.92[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap]
rs11078921	0.80[JPT][hapmap]
rs11078925	0.96[CEU][hapmap]
rs11078926	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs11078927	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap]
rs11557466	0.95[CEU][hapmap]
rs11557467	0.81[CEU][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11658993	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11870965	0.96[CEU][hapmap]
rs12936231	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs12942330	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12946510	0.92[CEU][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290400	0.81[CEU][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap]
rs2305479	0.86[ASW][hapmap];0.82[CEU][hapmap];0.91[CHD][hapmap];0.81[TSI][hapmap]
rs2305480	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs2313430	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2941522	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2952140	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2952144	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3816470	0.94[CHD][hapmap];0.84[MEX][hapmap]
rs4794820	0.81[JPT][hapmap]
rs4795395	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4795397	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4795400	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs4795402	0.80[CHD][hapmap]
rs4795403	0.80[CHD][hapmap]
rs4795404	0.80[CHD][hapmap]
rs4795405	0.86[CHD][hapmap];0.96[MEX][hapmap]
rs7216389	0.86[ASW][hapmap];0.82[CEU][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap]
rs7219923	0.82[CEU][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap]
rs7224129	0.82[CEU][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs8069176	0.96[CEU][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs8076131	0.86[ASW][hapmap];0.89[CEU][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs869402	0.86[ASW][hapmap];0.82[CEU][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap]
rs907091	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303277	0.82[CEU][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9303281	0.82[CEU][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap]
rs9747973	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9909593	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]

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	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	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
3	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

Variant related diseases (count:1)

Disease	PMID	Source
Primary biliary cirrhosis	19458352	GWAS catalog

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs907092	ORMDL3	cis	parietal	SCAN
rs907092	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs907092	MED1	cis	cerebellum	SCAN
rs907092	PGAP3	cis	Thyroid	GTEx
rs907092	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs907092	CDC6	cis	cerebellum	SCAN
rs907092	DHRS11	cis	parietal	SCAN
rs907092	ORMDL3	cis	lymphoblastoid	seeQTL
rs907092	GSDMB	cis	parietal	SCAN
rs907092	MED24	cis	parietal	SCAN
rs907092	CDK12	cis	parietal	SCAN
rs907092	GSDMB	cis	cerebellum	SCAN
rs907092	GSDMB	cis	Whole Blood	GTEx
rs907092	IKZF3	cis	multi-tissue	Pritchard
rs907092	ORMDL3	cis	multi-tissue	Pritchard
rs907092	PIGW	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37912000-37930400	Weak transcription	Esophagus	oesophagus
2	chr17:37912800-37927400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:37913600-37926400	Genic enhancers	Fetal Thymus	thymus
4	chr17:37915800-37926000	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr17:37916000-37922400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr17:37917000-37922800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr17:37917000-37922800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:37917000-37925800	Genic enhancers	Thymus	Thymus
9	chr17:37917200-37923000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr17:37917600-37923000	Strong transcription	Primary B cells from cord blood	blood
11	chr17:37918400-37929400	Weak transcription	Colonic Mucosa	Colon
12	chr17:37919200-37923000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr17:37919200-37926000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr17:37919400-37922600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:37920000-37922800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr17:37920000-37930000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:37920600-37922800	Strong transcription	Primary T cells from cord blood	blood
18	chr17:37920800-37931000	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr17:37921000-37923600	Genic enhancers	GM12878-XiMat	blood
20	chr17:37921000-37923800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr17:37921000-37926600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
22	chr17:37921200-37926200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
23	chr17:37921400-37922600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr17:37921800-37922800	Genic enhancers	Spleen	Spleen
25	chr17:37922200-37925800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr17:37922200-37926800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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