Variant report

Variant	rs12939832
Chromosome Location	chr17:38064876-38064877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38063849..38066832-chr17:38082215..38084527,2	MCF-7	breast:
2	chr17:38063855..38068073-chr17:38135195..38137481,3	K562	blood:
3	chr17:38060550..38063532-chr17:38063812..38066612,2	K562	blood:

Variant related genes	Relation type
ENSG00000108344	Chromatin interaction
ENSG00000264968	Chromatin interaction
ENSG00000172057	Chromatin interaction
ENSG00000073605	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1008723	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1011082	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1031458	0.95[ASN][1000 genomes]
rs1031460	0.95[ASN][1000 genomes]
rs11078925	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11078926	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11078927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11078928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11557466	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11557467	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11650661	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11651596	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655198	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11655292	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11870965	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12103884	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453507	0.89[ASN][1000 genomes]
rs12603332	0.91[ASN][1000 genomes]
rs12709365	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12936231	0.99[ASN][1000 genomes]
rs12936409	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12946393	0.81[ASN][1000 genomes]
rs12949100	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12950209	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12950743	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13380815	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1453559	0.94[ASN][1000 genomes]
rs2290400	0.93[ASN][1000 genomes]
rs2305479	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305480	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2872516	0.91[ASN][1000 genomes]
rs34120102	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36000226	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3744246	0.81[ASN][1000 genomes]
rs4065275	0.91[ASN][1000 genomes]
rs4794820	0.89[ASN][1000 genomes]
rs4795397	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795399	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795400	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795401	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4795402	0.81[ASN][1000 genomes]
rs4795403	0.81[ASN][1000 genomes]
rs4795404	0.81[ASN][1000 genomes]
rs4795405	0.90[ASN][1000 genomes]
rs56380902	0.95[ASN][1000 genomes]
rs62067034	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6503524	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7216389	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7216558	0.95[ASN][1000 genomes]
rs7219923	0.95[ASN][1000 genomes]
rs7221605	0.95[ASN][1000 genomes]
rs7221814	0.85[AMR][1000 genomes]
rs7224129	0.91[ASN][1000 genomes]
rs7224908	0.81[ASN][1000 genomes]
rs7359623	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8065777	0.95[ASN][1000 genomes]
rs8067378	0.99[ASN][1000 genomes]
rs8069176	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8074437	0.93[ASN][1000 genomes]
rs8076131	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs869402	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs883770	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs921649	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs921650	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9303279	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9303280	0.95[ASN][1000 genomes]
rs9303281	0.95[ASN][1000 genomes]
rs9906951	0.97[ASN][1000 genomes]
rs9916765	0.81[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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12939832	PGAP3	cis	Esophagus Muscularis	GTEx
rs12939832	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs12939832	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs12939832	ORMDL3	cis	Whole Blood	GTEx
rs12939832	GSDMB	cis	Whole Blood	GTEx

Chromatin state (count:104 , 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	chr17:38056200-38065400	Weak transcription	Placenta	Placenta
5	chr17:38056800-38074600	Weak transcription	NH-A	brain
6	chr17:38057000-38068800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:38057200-38074400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr17:38057400-38075400	Weak transcription	HSMM	muscle
9	chr17:38057600-38076600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr17:38057800-38077600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr17:38058000-38065200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr17:38058000-38067600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:38058000-38074600	Weak transcription	Left Ventricle	heart
14	chr17:38058200-38076200	Weak transcription	Fetal Lung	lung
15	chr17:38058200-38077800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr17:38058400-38075400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr17:38058600-38075400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:38058600-38077400	Weak transcription	Colon Smooth Muscle	Colon
19	chr17:38058800-38071800	Weak transcription	Stomach Mucosa	stomach
20	chr17:38059000-38065200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr17:38059000-38070400	Strong transcription	Fetal Stomach	stomach
22	chr17:38059000-38071000	Strong transcription	Thymus	Thymus
23	chr17:38059000-38082400	Weak transcription	Psoas Muscle	Psoas
24	chr17:38059200-38070600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr17:38059200-38075400	Weak transcription	Brain Hippocampus Middle	brain
26	chr17:38059400-38074000	Weak transcription	Small Intestine	intestine
27	chr17:38059600-38065000	Weak transcription	Lung	lung
28	chr17:38059600-38067800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr17:38059800-38070800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr17:38059800-38077200	Weak transcription	Esophagus	oesophagus
31	chr17:38060000-38066600	Weak transcription	Brain Substantia Nigra	brain
32	chr17:38060000-38077400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr17:38060200-38065000	Weak transcription	Osteobl	bone
34	chr17:38060200-38065200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:38060200-38065800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr17:38060200-38071400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr17:38060400-38065200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr17:38060400-38065400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr17:38060400-38069600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr17:38060400-38069800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:38060400-38070800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr17:38060400-38071200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr17:38060400-38081600	Weak transcription	Fetal Brain Male	brain
44	chr17:38060600-38065400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:38060600-38073000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr17:38060800-38068000	Strong transcription	Adipose Nuclei	Adipose
47	chr17:38060800-38075600	Strong transcription	Primary T cells from cord blood	blood
48	chr17:38061000-38065000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr17:38061000-38065800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr17:38061000-38068200	Strong transcription	Rectal Mucosa Donor 29	rectum

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