Variant report

Variant	rs11078931
Chromosome Location	chr17:38147294-38147295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr17:38147274-38147384	GM12878	blood:	n/a	n/a
2	SRF	chr17:38147228-38147365	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38142439..38144844-chr17:38145990..38148406,3	K562	blood:
2	chr17:38142013..38147565-chr17:38148653..38154078,9	K562	blood:
3	chr17:38142640..38144944-chr17:38146364..38148406,3	K562	blood:
4	chr17:38139958..38142841-chr17:38144945..38147813,2	MCF-7	breast:
5	chr1:216898478..216901280-chr17:38145496..38147429,2	MCF-7	breast:

No data

Variant related genes	Relation type
PSMD3	TF binding region
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10445310	0.82[ASN][1000 genomes]
rs11078930	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078935	0.84[ASN][1000 genomes]
rs11078936	0.83[ASN][1000 genomes]
rs11654208	0.83[ASN][1000 genomes]
rs11655264	0.94[ASN][1000 genomes]
rs11655655	0.83[ASN][1000 genomes]
rs11658328	0.96[ASN][1000 genomes]
rs11867302	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12309	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12450800	0.95[ASN][1000 genomes]
rs12451547	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12451897	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12453334	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12453341	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12453343	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12453764	0.97[ASN][1000 genomes]
rs12601929	0.81[ASN][1000 genomes]
rs12602514	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12602854	0.81[ASN][1000 genomes]
rs12939682	0.83[ASN][1000 genomes]
rs12940405	0.94[ASN][1000 genomes]
rs2227319	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2227321	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2227333	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241244	0.96[ASN][1000 genomes]
rs2241245	0.96[ASN][1000 genomes]
rs2270401	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302774	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302777	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305481	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305482	0.92[ASN][1000 genomes]
rs25645	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3087852	0.94[ASN][1000 genomes]
rs34003767	0.83[ASN][1000 genomes]
rs34342173	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34453912	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34540281	0.81[ASN][1000 genomes]
rs34648856	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34933056	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35272691	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35982947	0.81[ASN][1000 genomes]
rs36071767	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3744245	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785550	0.96[ASN][1000 genomes]
rs3816472	0.96[ASN][1000 genomes]
rs3859187	0.96[ASN][1000 genomes]
rs3859189	0.94[ASN][1000 genomes]
rs3935281	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4065321	0.96[ASN][1000 genomes]
rs4072639	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4433838	0.96[ASN][1000 genomes]
rs66826786	0.82[ASN][1000 genomes]
rs7502971	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8066582	0.96[ASN][1000 genomes]
rs8070444	0.96[ASN][1000 genomes]
rs8071037	0.96[ASN][1000 genomes]
rs8073254	0.96[ASN][1000 genomes]
rs8075668	0.94[ASN][1000 genomes]
rs9898547	0.93[ASN][1000 genomes]
rs9915252	0.96[ASN][1000 genomes]
rs9916158	0.92[EUR][1000 genomes];0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11078931	GSDMA	cis	Esophagus Muscularis	GTEx
rs11078931	GSDMA	cis	Adipose Subcutaneous	GTEx
rs11078931	GSDMA	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38138600-38149200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:38138600-38154200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:38139200-38151400	Strong transcription	NHEK	skin
4	chr17:38139200-38154800	Strong transcription	Fetal Intestine Small	intestine
5	chr17:38139400-38152200	Strong transcription	K562	blood
6	chr17:38139400-38154400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:38139400-38155000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr17:38139600-38151200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr17:38139600-38153600	Strong transcription	HUVEC	blood vessel
10	chr17:38139600-38154400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr17:38139600-38154600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:38139600-38154800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:38139600-38155000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:38139600-38155200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:38139600-38155400	Strong transcription	Placenta	Placenta
16	chr17:38139600-38155600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:38139600-38155600	Strong transcription	Fetal Thymus	thymus
18	chr17:38139800-38153800	Strong transcription	Osteobl	bone
19	chr17:38139800-38154400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr17:38139800-38154400	Strong transcription	HMEC	breast
21	chr17:38139800-38154600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr17:38139800-38154600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:38139800-38154800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr17:38139800-38155000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:38139800-38155000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:38139800-38155000	Strong transcription	A549	lung
27	chr17:38139800-38155600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr17:38140000-38148800	Strong transcription	Liver	Liver
29	chr17:38140000-38150400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr17:38140000-38150400	Strong transcription	Fetal Muscle Leg	muscle
31	chr17:38140000-38151200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr17:38140000-38152400	Strong transcription	Adipose Nuclei	Adipose
33	chr17:38140000-38153800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:38140000-38153800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr17:38140000-38154200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr17:38140000-38154200	Strong transcription	Brain Germinal Matrix	brain
37	chr17:38140000-38154200	Strong transcription	Lung	lung
38	chr17:38140000-38154400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:38140000-38154400	Strong transcription	Right Ventricle	heart
40	chr17:38140000-38154600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:38140000-38154600	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr17:38140000-38154600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:38140000-38154600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr17:38140000-38154600	Strong transcription	Brain Hippocampus Middle	brain
45	chr17:38140000-38154600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr17:38140000-38154600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr17:38140000-38154600	Strong transcription	Fetal Intestine Large	intestine
48	chr17:38140000-38155000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr17:38140000-38155000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr17:38140000-38155000	Strong transcription	Rectal Smooth Muscle	rectum

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