Variant report

Variant	rs2305481
Chromosome Location	chr17:38138624-38138625
allele	A/G
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:13)
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	POLR2A	chr17:38137564-38139125	K562	blood:	n/a	n/a
2	CTCF	chr17:38135251-38138738	A549	lung:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38038617..38042523-chr17:38137576..38140223,3	K562	blood:
2	chr17:38136187..38139299-chr17:38140015..38144342,5	K562	blood:
3	chr17:38137253..38140627-chr17:38150200..38152697,4	MCF-7	breast:
4	chr17:38138604..38140537-chr17:38144740..38146417,2	K562	blood:
5	chr17:38073305..38078163-chr17:38135913..38140017,5	K562	blood:
6	chr17:38117802..38119525-chr17:38136512..38138841,3	K562	blood:
7	chr17:38137876..38139862-chr17:38253958..38255577,2	K562	blood:
8	chr17:38094255..38096841-chr17:38137196..38138815,2	MCF-7	breast:
9	chr17:38107027..38109287-chr17:38138129..38139921,2	K562	blood:
10	chr17:38136308..38139120-chr17:38254735..38257246,2	MCF-7	breast:
11	chr17:38073305..38078633-chr17:38135671..38140017,6	K562	blood:
12	chr17:38137113..38139548-chr17:38217878..38220392,2	K562	blood:
13	chr17:38039742..38042523-chr17:38137576..38139684,2	K562	blood:

No data

Variant related genes	Relation type
PSMD3	TF binding region
ENSG00000108344	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000073605	Chromatin interaction
ENSG00000167914	Chromatin interaction
ENSG00000172057	Chromatin interaction
ENSG00000126351	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10445310	0.81[ASN][1000 genomes]
rs11078930	0.80[CEU][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11078931	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078935	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11078936	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11654208	0.83[ASN][1000 genomes]
rs11655264	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs11655655	0.83[ASN][1000 genomes]
rs11658328	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11867302	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11870683	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12309	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12450800	0.93[ASN][1000 genomes]
rs12451547	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12451897	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12453334	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453341	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12453343	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12453764	0.95[ASN][1000 genomes]
rs12601929	0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs12602514	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12602854	0.80[ASN][1000 genomes]
rs12939682	0.83[ASN][1000 genomes]
rs12940405	0.95[ASN][1000 genomes]
rs2227319	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2227321	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2227333	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241244	0.96[ASN][1000 genomes]
rs2241245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2270401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302774	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302776	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2302777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305482	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs25645	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3087852	0.98[ASN][1000 genomes]
rs34003767	0.83[ASN][1000 genomes]
rs34342173	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34453912	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34540281	0.80[ASN][1000 genomes]
rs34648856	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34933056	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35272691	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35982947	0.80[ASN][1000 genomes]
rs36071767	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3744245	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785550	0.92[ASN][1000 genomes]
rs3816472	0.96[ASN][1000 genomes]
rs3859187	0.96[ASN][1000 genomes]
rs3859189	0.98[ASN][1000 genomes]
rs3935281	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4065321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4072639	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4433838	0.96[ASN][1000 genomes]
rs66826786	0.81[ASN][1000 genomes]
rs7502971	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8066582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8070444	0.96[ASN][1000 genomes]
rs8071037	0.96[ASN][1000 genomes]
rs8073254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8075668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8077456	0.84[JPT][hapmap]
rs9898547	0.96[ASN][1000 genomes]
rs9915252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9916158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[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
rs2305481	GSDMA	cis	Esophagus Muscularis	GTEx
rs2305481	GSDMA	cis	Adipose Subcutaneous	GTEx
rs2305481	GSDMA	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38136200-38139000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr17:38137400-38138800	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr17:38137400-38138800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:38137400-38138800	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr17:38137400-38138800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr17:38137600-38139000	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr17:38137800-38138800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:38137800-38138800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr17:38137800-38139000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr17:38137800-38139200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr17:38137800-38139200	Transcr. at gene 5' and 3'	NHEK	skin
12	chr17:38137800-38140400	Weak transcription	Spleen	Spleen
13	chr17:38137800-38140600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:38138000-38138800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr17:38138000-38139000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr17:38138000-38139000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr17:38138000-38139200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:38138000-38139200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:38138200-38138800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:38138200-38138800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr17:38138200-38138800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr17:38138200-38138800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr17:38138200-38138800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr17:38138200-38138800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr17:38138200-38138800	Transcr. at gene 5' and 3'	Dnd41	blood
26	chr17:38138200-38139000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr17:38138200-38139000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:38138200-38139000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:38138200-38139000	Enhancers	Primary B cells from peripheral blood	blood
30	chr17:38138200-38139000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr17:38138200-38139200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:38138200-38139200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr17:38138200-38139200	Transcr. at gene 5' and 3'	K562	blood
34	chr17:38138200-38139200	Flanking Active TSS	NHDF-Ad	bronchial
35	chr17:38138200-38140000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:38138200-38140400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr17:38138200-38140600	Weak transcription	Aorta	Aorta
38	chr17:38138400-38138800	Flanking Active TSS	Fetal Brain Female	brain
39	chr17:38138400-38138800	Enhancers	Stomach Mucosa	stomach
40	chr17:38138400-38138800	Flanking Active TSS	HepG2	liver
41	chr17:38138400-38139000	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr17:38138400-38139000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:38138400-38139000	Enhancers	Fetal Heart	heart
44	chr17:38138400-38139000	Active TSS	Psoas Muscle	Psoas
45	chr17:38138400-38139000	Flanking Active TSS	GM12878-XiMat	blood
46	chr17:38138400-38139600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr17:38138400-38139800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr17:38138400-38139800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr17:38138400-38140000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr17:38138400-38140000	Weak transcription	Fetal Muscle Trunk	muscle

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