Variant report

Variant	rs12603332
Chromosome Location	chr17:38082807-38082808
allele	C/T
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	POLR2A	chr17:38082655-38084861	HepG2	liver:	n/a	n/a
2	CREB1	chr17:38082660-38084602	GM12878	blood:	n/a	n/a
3	HNF4G	chr17:38082762-38083402	HepG2	liver:	n/a	chr17:38083206-38083218 chr17:38083206-38083218 chr17:38083206-38083218
4	TCF12	chr17:38082673-38082912	GM12878	blood:	n/a	n/a
5	TBP	chr17:38082777-38083207	HepG2	liver:	n/a	n/a
6	HEY1	chr17:38082704-38084446	HepG2	liver:	n/a	chr17:38083885-38083900
7	PML	chr17:38082686-38083384	GM12878	blood:	n/a	n/a
8	TAF1	chr17:38082714-38082990	GM12878	blood:	n/a	n/a
9	HDAC2	chr17:38082638-38083413	HepG2	liver:	n/a	n/a
10	HDAC2	chr17:38082763-38083468	HepG2	liver:	n/a	n/a
11	NFYB	chr17:38082780-38082910	GM12878	blood:	n/a	n/a
12	POLR2A	chr17:38082545-38084314	GM12878	blood:	n/a	n/a
13	STAT5A	chr17:38082764-38083469	GM12878	blood:	n/a	chr17:38083356-38083368
14	POLR2A	chr17:38082407-38083485	GM12878	blood:	n/a	n/a
15	MYBL2	chr17:38082609-38083502	HepG2	liver:	n/a	n/a
16	CREB1	chr17:38082638-38084726	HepG2	liver:	n/a	n/a
17	MTA3	chr17:38082426-38085085	GM12878	blood:	n/a	n/a
18	RXRA	chr17:38082715-38083390	HepG2	liver:	n/a	chr17:38083206-38083220
19	YY1	chr17:38082664-38084525	HepG2	liver:	n/a	chr17:38083355-38083366 chr17:38083650-38083664 chr17:38083773-38083787
20	EP300	chr17:38082648-38083454	HepG2	liver:	n/a	n/a
21	EBF1	chr17:38082649-38083002	GM12878	blood:	n/a	n/a
22	POLR2A	chr17:38082689-38084594	GM19193	blood:	n/a	n/a
23	POLR2A	chr17:38082695-38085190	GM18505	blood:	n/a	n/a
24	POLR2A	chr17:38082751-38083326	HL-60	blood:	n/a	n/a
25	POLR2A	chr17:38082598-38084553	HepG2	liver:	n/a	n/a
26	ELF1	chr17:38082728-38084133	GM12878	blood:	n/a	chr17:38083353-38083365 chr17:38083780-38083792
27	FOXA1	chr17:38082683-38084111	HepG2	liver:	n/a	n/a
28	MAZ	chr17:38082781-38084482	HepG2	liver:	n/a	chr17:38083544-38083554 chr17:38083010-38083021
29	CEBPB	chr17:38082675-38083029	HepG2	liver:	n/a	n/a
30	NR2F2	chr17:38082735-38084415	K562	blood:	n/a	chr17:38083198-38083213
31	POLR2A	chr17:38082607-38084575	GM19099	blood:	n/a	n/a
32	POLR2A	chr17:38082748-38083267	GM12892	blood:	n/a	n/a
33	CEBPB	chr17:38082707-38082987	HepG2	liver:	n/a	n/a
34	RUNX3	chr17:38082525-38083446	GM12878	blood:	n/a	n/a
35	HEY1	chr17:38082513-38084645	HepG2	liver:	n/a	chr17:38083885-38083900
36	MYBL2	chr17:38082793-38083500	HepG2	liver:	n/a	n/a
37	SP1	chr17:38082700-38083483	HepG2	liver:	n/a	chr17:38083362-38083372 chr17:38082922-38082936 chr17:38083165-38083176 chr17:38083361-38083373 chr17:38083362-38083371 chr17:38083358-38083372 chr17:38082921-38082933 chr17:38082909-38082923 chr17:38083361-38083373
38	POLR2A	chr17:38082686-38084127	GM12878	blood:	n/a	n/a
39	POLR2A	chr17:38082542-38083304	HepG2	liver:	n/a	n/a
40	MXI1	chr17:38082769-38084529	HepG2	liver:	n/a	n/a
41	MAZ	chr17:38082700-38083324	GM12878	blood:	n/a	chr17:38083010-38083021
42	MBD4	chr17:38082486-38083318	HepG2	liver:	n/a	n/a
43	POLR2A	chr17:38082704-38084603	HepG2	liver:	n/a	n/a
44	POLR2A	chr17:38082578-38083399	GM12892	blood:	n/a	n/a
45	POLR2A	chr17:38082472-38085031	HepG2	liver:	n/a	n/a
46	MBD4	chr17:38082779-38083446	HepG2	liver:	n/a	n/a
47	TEAD4	chr17:38082754-38083430	HepG2	liver:	n/a	n/a
48	WRNIP1	chr17:38082239-38082911	GM12878	blood:	n/a	n/a
49	NFIC	chr17:38082632-38084590	HepG2	liver:	n/a	chr17:38083922-38083950
50	POLR2A	chr17:38082594-38085130	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38063849..38066832-chr17:38082215..38084527,2	MCF-7	breast:
2	chr17:38082350..38085117-chr17:38171214..38173786,2	K562	blood:
3	chr17:38082705..38085668-chr17:38094969..38098446,5	K562	blood:
4	chr17:38080996..38082970-chr17:38254753..38256927,2	MCF-7	breast:
5	chr17:38082095..38085117-chr17:38171214..38173786,3	K562	blood:

Variant related genes	Relation type
ORMDL3	TF binding region
ENSG00000264968	TF binding region
ENSG00000073605	Chromatin interaction
ENSG00000204913	Chromatin interaction
ENSG00000108342	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1008723	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1011082	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1031458	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1031460	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10445308	0.90[CHB][hapmap]
rs10852936	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11078925	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11078926	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11078927	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11078928	0.92[ASN][1000 genomes]
rs11557466	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11557467	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11650661	0.92[ASN][1000 genomes]
rs11651596	0.91[ASN][1000 genomes]
rs11655198	0.92[ASN][1000 genomes]
rs11655292	0.92[ASN][1000 genomes]
rs11870965	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12103884	0.92[ASN][1000 genomes]
rs12453507	0.85[ASN][1000 genomes]
rs12709365	0.92[ASN][1000 genomes]
rs12936231	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12936409	0.91[ASN][1000 genomes]
rs12939832	0.91[ASN][1000 genomes]
rs12946393	0.90[ASN][1000 genomes]
rs12946510	0.90[CHB][hapmap]
rs12949100	0.92[ASN][1000 genomes]
rs12950209	0.92[ASN][1000 genomes]
rs12950743	0.92[ASN][1000 genomes]
rs13380815	0.92[ASN][1000 genomes]
rs1453559	0.90[ASN][1000 genomes]
rs2290400	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305479	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2305480	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2872516	0.91[ASN][1000 genomes]
rs34120102	0.92[ASN][1000 genomes]
rs36000226	0.92[ASN][1000 genomes]
rs3744246	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3816470	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4065275	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794820	0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795397	0.90[ASN][1000 genomes]
rs4795399	0.92[ASN][1000 genomes]
rs4795400	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4795401	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795402	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4795403	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4795404	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4795405	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56380902	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62067034	0.92[ASN][1000 genomes]
rs6503524	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7216389	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7216558	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7219923	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7221605	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7221814	0.87[ASN][1000 genomes]
rs7224129	0.82[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7224908	0.90[ASN][1000 genomes]
rs7359623	0.92[ASN][1000 genomes]
rs8065777	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8067378	0.92[ASN][1000 genomes]
rs8069176	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8074437	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8076131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs869402	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs883770	0.92[ASN][1000 genomes]
rs907091	0.85[CHB][hapmap]
rs921649	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs921650	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303277	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs9303279	0.95[ASN][1000 genomes]
rs9303280	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303281	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9635726	0.95[CHB][hapmap]
rs9906951	0.89[ASN][1000 genomes]
rs9909593	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12603332	ORMDL3	cis	Whole Blood	GTEx
rs12603332	GSDMA	cis	Nerve Tibial	GTEx
rs12603332	ORMDL3	cis	Lymphoblastoid	GTEx
rs12603332	PGAP3	cis	Esophagus Muscularis	GTEx
rs12603332	IKZF3	cis	multi-tissue	Pritchard
rs12603332	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs12603332	GSDMA	cis	Adipose Subcutaneous	GTEx
rs12603332	GSDMA	cis	lung	GTEx
rs12603332	ORMDL3	cis	multi-tissue	Pritchard
rs12603332	RP11-387H17.4	cis	Muscle Skeletal	GTEx
rs12603332	GSDMB	cis	Whole Blood	GTEx
rs12603332	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38080000-38083000	Weak transcription	Ovary	ovary
2	chr17:38080600-38083000	Weak transcription	Aorta	Aorta
3	chr17:38080600-38083000	Enhancers	Lung	lung
4	chr17:38080800-38083000	Enhancers	Gastric	stomach
5	chr17:38080800-38083400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr17:38081000-38083000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr17:38081000-38083200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr17:38081200-38083200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr17:38081200-38083400	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr17:38081200-38083600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:38081400-38083000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:38081400-38083400	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr17:38081600-38083000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:38081600-38083000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr17:38081600-38083000	Enhancers	Esophagus	oesophagus
16	chr17:38081600-38083000	Enhancers	Spleen	Spleen
17	chr17:38081600-38083400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr17:38081800-38083000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr17:38081800-38083400	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr17:38081800-38083400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr17:38082000-38083000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr17:38082000-38083200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr17:38082000-38083200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr17:38082000-38083200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr17:38082000-38083200	Flanking Active TSS	Dnd41	blood
26	chr17:38082200-38083000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr17:38082200-38083000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:38082200-38083000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:38082200-38083200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr17:38082200-38083200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:38082200-38083200	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr17:38082200-38083200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr17:38082200-38083400	Flanking Active TSS	Placenta	Placenta
34	chr17:38082200-38083400	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr17:38082200-38083600	Flanking Active TSS	Colonic Mucosa	Colon
36	chr17:38082200-38084200	Active TSS	Thymus	Thymus
37	chr17:38082400-38083000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr17:38082400-38083000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr17:38082400-38083000	Flanking Active TSS	Fetal Lung	lung
40	chr17:38082400-38083000	Enhancers	Psoas Muscle	Psoas
41	chr17:38082400-38083000	Flanking Active TSS	HMEC	breast
42	chr17:38082400-38083000	Flanking Active TSS	NHDF-Ad	bronchial
43	chr17:38082400-38083200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:38082400-38083200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr17:38082400-38083200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:38082400-38083200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr17:38082400-38083200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr17:38082400-38083200	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr17:38082400-38083200	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr17:38082400-38083200	Flanking Active TSS	Fetal Stomach	stomach

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