Variant report

Variant	rs17609240
Chromosome Location	chr17:38110689-38110690
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38082186..38086567-chr17:38107763..38110832,6	K562	blood:
2	chr17:38108082..38110998-chr17:38277597..38279860,2	K562	blood:
3	chr17:38107392..38113362-chr17:38135377..38138663,7	K562	blood:
4	chr17:38107835..38110807-chr17:38134929..38137852,3	K562	blood:
5	chr17:38082186..38083715-chr17:38108086..38110832,2	K562	blood:
6	chr17:38090703..38093615-chr17:38109038..38110854,2	K562	blood:
7	chr17:38109945..38111451-chr17:38115405..38117518,2	K562	blood:
8	chr17:38108595..38111573-chr17:38115257..38117518,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108344	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000172057	Chromatin interaction
ENSG00000264968	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1007654	0.94[CEU][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1007655	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11869855	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1563103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2001476	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2313640	0.94[CEU][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28618095	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3848395	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3902024	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3931960	0.90[ASN][1000 genomes]
rs4134501	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4458030	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55860944	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56301252	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56396280	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60667221	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62068174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62068175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62068176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62068177	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62068178	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62068179	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62068180	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62068181	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62068182	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62068183	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62068184	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6503527	0.94[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7207600	0.94[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7209742	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7218321	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7218742	0.94[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7219080	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7223318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8065126	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8068522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8071050	0.88[ASN][1000 genomes]
rs8076474	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8081437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9889711	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9889716	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9895948	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3442992	chr17:38107951-38110799	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Hematological parameters	19820697	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17609240	GSDMA	cis	Esophagus Muscularis	GTEx
rs17609240	GSDMA	cis	Adipose Subcutaneous	GTEx
rs17609240	GSDMA	cis	lung	GTEx
rs17609240	GSDMA	cis	Artery Tibial	GTEx
rs17609240	GSDMA	cis	Thyroid	GTEx
rs17609240	GSDMA	cis	Artery Aorta	GTEx
rs17609240	GSDMA	cis	Nerve Tibial	GTEx
rs17609240	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38108400-38110800	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr17:38109000-38111200	Enhancers	Primary B cells from cord blood	blood
3	chr17:38110000-38115400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr17:38110000-38115400	Weak transcription	Osteobl	bone
5	chr17:38110000-38118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:38110200-38110800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:38110200-38110800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr17:38110200-38110800	Enhancers	Primary B cells from peripheral blood	blood
9	chr17:38110200-38110800	Enhancers	Fetal Brain Male	brain
10	chr17:38110200-38110800	Enhancers	Gastric	stomach
11	chr17:38110200-38110800	Enhancers	GM12878-XiMat	blood
12	chr17:38110200-38111200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:38110200-38111200	Weak transcription	Fetal Thymus	thymus
14	chr17:38110200-38111200	Enhancers	HepG2	liver
15	chr17:38110200-38111400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr17:38110200-38111400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr17:38110200-38111400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:38110200-38111400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:38110200-38111400	Enhancers	K562	blood
20	chr17:38110200-38112200	Weak transcription	Fetal Muscle Leg	muscle
21	chr17:38110200-38115000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr17:38110200-38115000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr17:38110200-38115000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr17:38110200-38115000	Weak transcription	Colonic Mucosa	Colon
25	chr17:38110200-38115000	Weak transcription	NHEK	skin
26	chr17:38110200-38115200	Weak transcription	Primary T cells from cord blood	blood
27	chr17:38110200-38115200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr17:38110200-38115200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:38110200-38115200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr17:38110200-38115200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:38110200-38115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:38110200-38115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr17:38110200-38115200	Weak transcription	Adipose Nuclei	Adipose
34	chr17:38110200-38115200	Weak transcription	Liver	Liver
35	chr17:38110200-38115200	Weak transcription	Brain Angular Gyrus	brain
36	chr17:38110200-38115200	Weak transcription	Colon Smooth Muscle	Colon
37	chr17:38110200-38115200	Weak transcription	Fetal Intestine Large	intestine
38	chr17:38110200-38115200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr17:38110200-38115200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr17:38110200-38115200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr17:38110200-38115200	Weak transcription	HMEC	breast
42	chr17:38110200-38115200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr17:38110200-38115400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr17:38110200-38115400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:38110200-38115400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:38110200-38115400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr17:38110200-38115400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr17:38110200-38115400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr17:38110200-38115400	Weak transcription	Fetal Intestine Small	intestine
50	chr17:38110200-38115400	Weak transcription	Stomach Mucosa	stomach

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