Variant report

Variant	rs62068178
Chromosome Location	chr17:38112608-38112609
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	chr17:38107392..38113362-chr17:38135377..38138663,7	K562	blood:

Variant related genes	Relation type
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1007654	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1007655	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11869855	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1563103	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17609240	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2001476	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2313640	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28618095	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3848395	0.83[EUR][1000 genomes]
rs3902024	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3931960	0.83[ASN][1000 genomes]
rs4134501	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4458030	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56301252	0.85[AMR][1000 genomes]
rs56396280	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60667221	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62068174	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62068175	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62068176	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62068177	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62068179	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62068180	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62068181	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62068182	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62068183	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62068184	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6503527	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7207600	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7209742	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7218321	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7218742	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7219080	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7223318	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8065126	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8068522	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8071050	0.82[ASN][1000 genomes]
rs8076474	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8081437	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9889711	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9889716	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9895948	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62068178	GSDMA	cis	lung	GTEx
rs62068178	GSDMA	cis	Artery Tibial	GTEx
rs62068178	GSDMA	cis	Esophagus Muscularis	GTEx
rs62068178	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs62068178	GSDMA	cis	Artery Aorta	GTEx
rs62068178	GSDMA	cis	Nerve Tibial	GTEx
rs62068178	GSDMA	cis	Thyroid	GTEx
rs62068178	GSDMA	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38110000-38115400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr17:38110000-38115400	Weak transcription	Osteobl	bone
3	chr17:38110000-38118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:38110200-38115000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr17:38110200-38115000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:38110200-38115000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr17:38110200-38115000	Weak transcription	Colonic Mucosa	Colon
8	chr17:38110200-38115000	Weak transcription	NHEK	skin
9	chr17:38110200-38115200	Weak transcription	Primary T cells from cord blood	blood
10	chr17:38110200-38115200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:38110200-38115200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:38110200-38115200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr17:38110200-38115200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:38110200-38115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:38110200-38115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:38110200-38115200	Weak transcription	Adipose Nuclei	Adipose
17	chr17:38110200-38115200	Weak transcription	Liver	Liver
18	chr17:38110200-38115200	Weak transcription	Brain Angular Gyrus	brain
19	chr17:38110200-38115200	Weak transcription	Colon Smooth Muscle	Colon
20	chr17:38110200-38115200	Weak transcription	Fetal Intestine Large	intestine
21	chr17:38110200-38115200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr17:38110200-38115200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr17:38110200-38115200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr17:38110200-38115200	Weak transcription	HMEC	breast
25	chr17:38110200-38115200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr17:38110200-38115400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr17:38110200-38115400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr17:38110200-38115400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:38110200-38115400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr17:38110200-38115400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr17:38110200-38115400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr17:38110200-38115400	Weak transcription	Fetal Intestine Small	intestine
33	chr17:38110200-38115400	Weak transcription	Stomach Mucosa	stomach
34	chr17:38110200-38115400	Weak transcription	Hela-S3	cervix
35	chr17:38110200-38116600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr17:38110200-38118600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr17:38110200-38118600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr17:38110400-38115200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr17:38110400-38115200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr17:38110400-38115200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr17:38110400-38115200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr17:38110400-38115200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr17:38110400-38115400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:38110400-38115400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr17:38110600-38115200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr17:38110800-38115000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr17:38110800-38115000	Weak transcription	GM12878-XiMat	blood
48	chr17:38110800-38115400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr17:38110800-38128800	Weak transcription	Gastric	stomach
50	chr17:38111200-38115000	Weak transcription	Primary B cells from cord blood	blood

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