Variant report

Variant	rs7216389
Chromosome Location	chr17:38069949-38069950
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	chr17:38068952..38070960-chr17:38079327..38082033,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172057	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1008723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1011082	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1031458	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1031460	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10445308	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap]
rs10852936	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs11078925	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11078926	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11078927	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11078928	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11557466	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11557467	1.00[CEU][hapmap];1.00[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];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11650661	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11651596	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11655198	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11655292	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11870965	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12103884	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12453507	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12603332	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12709365	0.96[ASN][1000 genomes]
rs12936231	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]
rs12936409	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12939832	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12946393	0.85[ASN][1000 genomes]
rs12946510	0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[MEX][hapmap]
rs12949100	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12950209	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12950743	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13380815	0.96[ASN][1000 genomes]
rs1453559	0.94[ASN][1000 genomes]
rs2290400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305479	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305480	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2872516	0.96[ASN][1000 genomes]
rs34120102	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs36000226	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3744246	0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs3816470	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs4065275	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4794820	0.90[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs4795397	0.82[CEU][hapmap];0.94[ASN][1000 genomes]
rs4795399	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4795400	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795401	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795402	0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4795403	0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4795404	0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4795405	0.91[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs56380902	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62067034	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6503524	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213668	0.84[ASN][1000 genomes]
rs7216558	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219923	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221605	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7221814	0.83[ASN][1000 genomes]
rs7224129	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7224908	0.85[ASN][1000 genomes]
rs7359623	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8065777	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8067378	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8069176	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.96[ASN][1000 genomes]
rs8074437	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8076131	1.00[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs869402	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883770	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907091	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap]
rs907092	0.86[ASW][hapmap];0.82[CEU][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap]
rs921649	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921650	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303277	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap]
rs9303279	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9303280	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9635726	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs9906951	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9909593	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs9916765	0.82[ASN][1000 genomes]

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

Variant related diseases (count:1)

Disease	PMID	Source
Asthma	17611496	GWAS catalog

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs7216389	GSDML	cis	multi-tissue	Pritchard
rs7216389	GSDMB	cis	parietal	SCAN
rs7216389	MED24	cis	parietal	SCAN
rs7216389	IKZF3	cis	multi-tissue	Pritchard
rs7216389	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs7216389	CDC6	cis	cerebellum	SCAN
rs7216389	ORMDL3	cis	lymphoblastoid	seeQTL
rs7216389	DHRS11	cis	parietal	SCAN
rs7216389	KRT222	cis	cerebellum	SCAN
rs7216389	ORMDL3	cis	parietal	SCAN
rs7216389	CDK12	cis	parietal	SCAN
rs7216389	MED1	cis	cerebellum	SCAN
rs7216389	MED24	cis	cerebellum	SCAN
rs7216389	ZNHIT3	cis	cerebellum	SCAN
rs7216389	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs7216389	SNORA21	cis	parietal	SCAN
rs7216389	GSDMB	cis	Whole Blood	GTEx
rs7216389	ORMDL3	cis	Lymphoblastoid	GTEx
rs7216389	ORMDL3	cis	multi-tissue	Pritchard
rs7216389	ORMDL3	cis	lymphoblastoid	GTEx
rs7216389	GSDMB	cis	cerebellum	SCAN
rs7216389	ORMDL3	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38049200-38075400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr17:38052600-38074200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:38055600-38077400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:38056800-38074600	Weak transcription	NH-A	brain
5	chr17:38057200-38074400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr17:38057400-38075400	Weak transcription	HSMM	muscle
7	chr17:38057600-38076600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr17:38057800-38077600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr17:38058000-38074600	Weak transcription	Left Ventricle	heart
10	chr17:38058200-38076200	Weak transcription	Fetal Lung	lung
11	chr17:38058200-38077800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:38058400-38075400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:38058600-38075400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:38058600-38077400	Weak transcription	Colon Smooth Muscle	Colon
15	chr17:38058800-38071800	Weak transcription	Stomach Mucosa	stomach
16	chr17:38059000-38070400	Strong transcription	Fetal Stomach	stomach
17	chr17:38059000-38071000	Strong transcription	Thymus	Thymus
18	chr17:38059000-38082400	Weak transcription	Psoas Muscle	Psoas
19	chr17:38059200-38070600	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:38059200-38075400	Weak transcription	Brain Hippocampus Middle	brain
21	chr17:38059400-38074000	Weak transcription	Small Intestine	intestine
22	chr17:38059800-38070800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr17:38059800-38077200	Weak transcription	Esophagus	oesophagus
24	chr17:38060000-38077400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr17:38060200-38071400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:38060400-38070800	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr17:38060400-38071200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr17:38060400-38081600	Weak transcription	Fetal Brain Male	brain
29	chr17:38060600-38073000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr17:38060800-38075600	Strong transcription	Primary T cells from cord blood	blood
31	chr17:38061000-38072800	Weak transcription	K562	blood
32	chr17:38061000-38074200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr17:38061200-38074000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:38061400-38075400	Weak transcription	Right Ventricle	heart
35	chr17:38061600-38070800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr17:38061600-38071600	Strong transcription	Fetal Intestine Small	intestine
37	chr17:38061600-38074200	Strong transcription	Fetal Thymus	thymus
38	chr17:38061800-38081000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:38062200-38075200	Weak transcription	Spleen	Spleen
40	chr17:38062200-38075400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr17:38062400-38075400	Weak transcription	Dnd41	blood
42	chr17:38062800-38078200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr17:38063000-38070800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:38063600-38077000	Weak transcription	Pancreas	Pancrea
45	chr17:38063800-38074200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr17:38063800-38075400	Weak transcription	NHEK	skin
47	chr17:38064000-38075200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr17:38065000-38070600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr17:38065000-38073400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr17:38065400-38070600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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