Variant report

Variant	rs55860944
Chromosome Location	chr17:38109302-38109303
allele	A/G
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37978424..37980112-chr17:38107868..38109558,2	K562	blood:
2	chr17:38107709..38109342-chr17:38252827..38255550,2	K562	blood:
3	chr17:38101089..38105078-chr17:38105781..38110100,7	K562	blood:
4	chr17:38107864..38109571-chr17:38137036..38138618,2	MCF-7	breast:
5	chr17:38082186..38086567-chr17:38107763..38110832,6	K562	blood:
6	chr17:38108082..38110998-chr17:38277597..38279860,2	K562	blood:
7	chr17:38107392..38113362-chr17:38135377..38138663,7	K562	blood:
8	chr17:38097357..38100615-chr17:38107229..38110087,5	K562	blood:
9	chr17:38107835..38110807-chr17:38134929..38137852,3	K562	blood:
10	chr17:38082601..38085339-chr17:38107879..38109914,2	MCF-7	breast:
11	chr17:38082186..38083715-chr17:38108086..38110832,2	K562	blood:
12	chr17:38109093..38109721-chr17:38136840..38137595,2	K562	blood:
13	chr17:38090703..38093615-chr17:38109038..38110854,2	K562	blood:
14	chr17:38108595..38111573-chr17:38115257..38117518,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264968	Chromatin interaction
ENSG00000204913	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000172057	Chromatin interaction
ENSG00000188895	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1007654	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1007655	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11869855	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1563103	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17609240	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001476	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2313640	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28618095	0.84[EUR][1000 genomes]
rs3848395	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3902024	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3931960	0.81[ASN][1000 genomes]
rs4134501	0.82[AMR][1000 genomes]
rs4458030	0.82[EUR][1000 genomes]
rs56396280	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60667221	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62068174	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62068175	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62068176	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62068180	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62068181	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62068182	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62068183	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62068184	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6503527	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7207600	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7209742	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7218321	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7218742	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7219080	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7223318	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8065126	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8068522	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8071050	0.81[ASN][1000 genomes]
rs8076474	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8081437	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9889711	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9889716	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9895948	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv3410693	chr17:38108326-38110574	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv3420775	chr17:38108776-38110124	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs55860944	GSDMA	cis	Artery Tibial	GTEx
rs55860944	GSDMA	cis	lung	GTEx
rs55860944	GSDMA	cis	Adipose Subcutaneous	GTEx
rs55860944	GSDMA	cis	Artery Aorta	GTEx
rs55860944	GSDMA	cis	Thyroid	GTEx
rs55860944	GSDMA	cis	Esophagus Muscularis	GTEx
rs55860944	GSDMA	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38108400-38109600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr17:38108400-38109600	Enhancers	Esophagus	oesophagus
3	chr17:38108400-38109800	Active TSS	Brain Cingulate Gyrus	brain
4	chr17:38108400-38109800	Active TSS	Brain Substantia Nigra	brain
5	chr17:38108400-38110800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr17:38108600-38109600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:38108600-38109600	Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr17:38108600-38109600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr17:38108600-38109600	Active TSS	Brain Germinal Matrix	brain
10	chr17:38108600-38109600	Enhancers	HMEC	breast
11	chr17:38108600-38109600	Enhancers	HUVEC	blood vessel
12	chr17:38108600-38109800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr17:38108600-38109800	Active TSS	Fetal Kidney	kidney
14	chr17:38108600-38110000	Active TSS	Brain Anterior Caudate	brain
15	chr17:38108600-38110200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr17:38108600-38110200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr17:38108800-38109800	Active TSS	Brain Angular Gyrus	brain
18	chr17:38108800-38109800	Active TSS	Fetal Brain Female	brain
19	chr17:38108800-38109800	Active TSS	Gastric	stomach
20	chr17:38108800-38109800	Active TSS	Ovary	ovary
21	chr17:38108800-38109800	Active TSS	A549	lung
22	chr17:38108800-38110000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr17:38108800-38110000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr17:38108800-38110000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:38108800-38110000	Active TSS	Right Ventricle	heart
26	chr17:38108800-38110400	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr17:38108800-38110400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr17:38109000-38109400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr17:38109000-38109400	Genic enhancers	Right Atrium	heart
30	chr17:38109000-38109600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr17:38109000-38109600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:38109000-38109600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr17:38109000-38109600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr17:38109000-38109600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr17:38109000-38109600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr17:38109000-38109600	Active TSS	Primary monocytes fromperipheralblood	blood
37	chr17:38109000-38109600	Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr17:38109000-38109600	Enhancers	Primary T cells from cord blood	blood
39	chr17:38109000-38109600	Enhancers	Primary hematopoietic stem cells	blood
40	chr17:38109000-38109600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr17:38109000-38109600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr17:38109000-38109600	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr17:38109000-38109600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr17:38109000-38109600	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr17:38109000-38109600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr17:38109000-38109600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr17:38109000-38109600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr17:38109000-38109600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr17:38109000-38109600	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr17:38109000-38109600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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