Variant report

Variant	rs56922390
Chromosome Location	chr17:38157021-38157022
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1042658	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1045929	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11078934	0.87[EUR][1000 genomes]
rs11871747	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12600856	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602172	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12941811	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2227315	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2227322	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2227336	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3213762	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3826331	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3935280	0.86[EUR][1000 genomes]
rs4794822	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794823	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4794824	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4795412	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795418	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4795419	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4795420	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55771023	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55846942	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57065891	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57968500	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59925331	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60082402	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62065177	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6503530	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7021	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709591	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs709592	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7208815	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7209755	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7214085	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7221894	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7222039	0.95[ASN][1000 genomes]
rs7502514	0.87[EUR][1000 genomes]
rs8065519	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8067817	0.95[ASN][1000 genomes]
rs8068260	0.90[ASN][1000 genomes]
rs8070454	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8072548	0.95[ASN][1000 genomes]
rs8078723	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8081692	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv908220	chr17:38153473-38175426	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs56922390	GSDMA	cis	Nerve Tibial	GTEx
rs56922390	MED24	cis	Nerve Tibial	GTEx
rs56922390	MED24	cis	Artery Aorta	GTEx
rs56922390	MED24	cis	Artery Tibial	GTEx
rs56922390	GSDMA	cis	Esophagus Muscularis	GTEx
rs56922390	GSDMA	cis	lung	GTEx
rs56922390	GSDMA	cis	Adipose Subcutaneous	GTEx
rs56922390	GSDMA	cis	Artery Aorta	GTEx
rs56922390	MED24	cis	Thyroid	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38147400-38157400	Weak transcription	Fetal Brain Male	brain
2	chr17:38150600-38157200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:38152200-38160600	Weak transcription	Psoas Muscle	Psoas
4	chr17:38152200-38160800	Weak transcription	K562	blood
5	chr17:38153200-38158400	Weak transcription	Fetal Kidney	kidney
6	chr17:38153200-38166400	Weak transcription	Fetal Lung	lung
7	chr17:38153400-38158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr17:38153400-38166200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr17:38153400-38166600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:38153600-38160400	Weak transcription	HSMMtube	muscle
11	chr17:38153600-38160600	Weak transcription	Stomach Mucosa	stomach
12	chr17:38153800-38160600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr17:38153800-38166200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:38153800-38166200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr17:38153800-38172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:38154200-38157200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr17:38154200-38157400	Weak transcription	Brain Germinal Matrix	brain
18	chr17:38154200-38161000	Weak transcription	Lung	lung
19	chr17:38154200-38166400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr17:38154400-38157200	Weak transcription	HMEC	breast
21	chr17:38154400-38157400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr17:38154400-38157600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr17:38154400-38157800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr17:38154400-38157800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr17:38154400-38158400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:38154400-38158800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr17:38154400-38160400	Weak transcription	HepG2	liver
28	chr17:38154400-38166200	Weak transcription	Dnd41	blood
29	chr17:38154400-38166400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr17:38154600-38157200	Weak transcription	Left Ventricle	heart
31	chr17:38154600-38158000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:38154600-38160800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr17:38154600-38166200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr17:38154600-38166400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:38154600-38170000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr17:38154600-38170200	Weak transcription	Esophagus	oesophagus
37	chr17:38154800-38157800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr17:38154800-38158800	Weak transcription	Fetal Intestine Small	intestine
39	chr17:38154800-38159200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr17:38154800-38173600	Weak transcription	Thymus	Thymus
41	chr17:38155000-38157200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr17:38155000-38157200	Weak transcription	Brain Angular Gyrus	brain
43	chr17:38155000-38157200	Weak transcription	GM12878-XiMat	blood
44	chr17:38155000-38157400	Weak transcription	Colon Smooth Muscle	Colon
45	chr17:38155000-38157400	Weak transcription	A549	lung
46	chr17:38155000-38157600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr17:38155000-38157600	Weak transcription	Brain Anterior Caudate	brain
48	chr17:38155000-38158000	Weak transcription	Primary T cells from cord blood	blood
49	chr17:38155000-38158400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr17:38155000-38158800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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