Variant report

Variant	rs9898547
Chromosome Location	chr17:38136026-38136027
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr17:38135829-38137232	K562	blood:	n/a	n/a
2	CEBPB	chr17:38135247-38136446	IMR90	lung:	n/a	chr17:38136203-38136216 chr17:38136203-38136214
3	GATA1	chr17:38135870-38138517	PBDE	blood:	n/a	n/a
4	CTCF	chr17:38135251-38138738	A549	lung:	n/a	n/a
5	CTCF	chr17:38136020-38136170	HCM	heart:	n/a	n/a
6	EP300	chr17:38135707-38137232	K562	blood:	n/a	chr17:38137006-38137020
7	CTCF	chr17:38135240-38138186	SK-N-SH	brain:	n/a	n/a
8	RUNX3	chr17:38136011-38137396	GM12878	blood:	n/a	n/a
9	RFX5	chr17:38135695-38137352	K562	blood:	n/a	chr17:38136745-38136760 chr17:38136748-38136757
10	CTCF	chr17:38135920-38136070	NHDF-neo	bronchial:	n/a	n/a
11	POLR2A	chr17:38135955-38137540	Raji	blood:	n/a	n/a
12	SIN3AK20	chr17:38135976-38137509	A549	lung:	n/a	n/a
13	UBTF	chr17:38135913-38137835	K562	blood:	n/a	n/a
14	CTCF	chr17:38136020-38136170	HMEC	breast:	n/a	n/a
15	RFX5	chr17:38135298-38137325	Hela-S3	cervix:	n/a	chr17:38136745-38136760 chr17:38136748-38136757
16	CEBPB	chr17:38136014-38136525	K562	blood:	n/a	chr17:38136203-38136216 chr17:38136203-38136214
17	RFX5	chr17:38134990-38138198	SK-N-SH	brain:	n/a	chr17:38136745-38136760 chr17:38136748-38136757
18	CREB1	chr17:38136010-38137401	K562	blood:	n/a	chr17:38136758-38136771
19	REST	chr17:38135913-38137814	H1-neurons	neurons:	n/a	chr17:38137569-38137582
20	RAD21	chr17:38135576-38137698	SK-N-SH	brain:	n/a	n/a
21	RFX5	chr17:38135752-38137225	GM12878	blood:	n/a	chr17:38136745-38136760 chr17:38136748-38136757
22	POLR2A	chr17:38135940-38138515	PBDE	blood:	n/a	n/a
23	NR2F2	chr17:38135679-38137330	K562	blood:	n/a	n/a
24	JUN	chr17:38135128-38137833	K562	blood:	n/a	chr17:38135339-38135349 chr17:38136759-38136772 chr17:38135339-38135349 chr17:38136760-38136769 chr17:38135339-38135349
25	CBX3	chr17:38135998-38137575	K562	blood:	n/a	n/a
26	RFX5	chr17:38135845-38137287	HepG2	liver:	n/a	chr17:38136745-38136760 chr17:38136748-38136757
27	RFX5	chr17:38135127-38137866	IMR90	lung:	n/a	chr17:38136745-38136760 chr17:38136748-38136757
28	MYBL2	chr17:38136003-38138039	HepG2	liver:	n/a	n/a
29	POLR2A	chr17:38135857-38137299	GM12891	blood:	n/a	n/a
30	TEAD4	chr17:38135944-38137891	K562	blood:	n/a	n/a
31	MTA3	chr17:38135991-38138024	GM12878	blood:	n/a	n/a
32	ATF1	chr17:38135777-38137197	K562	blood:	n/a	n/a
33	CEBPB	chr17:38136025-38136409	MCF-7	breast:	n/a	chr17:38136203-38136216 chr17:38136203-38136214
34	POLR2A	chr17:38135979-38137868	H1-hESC	embryonic stem cell:	n/a	n/a
35	SMC3	chr17:38135824-38137651	SK-N-SH	brain:	n/a	n/a
36	HCFC1	chr17:38135649-38138048	Hela-S3	cervix:	n/a	n/a
37	IRF1	chr17:38135875-38137291	K562	blood:	n/a	chr17:38135996-38136003
38	RFX5	chr17:38135917-38137383	H1-hESC	embryonic stem cell:	n/a	chr17:38136745-38136760 chr17:38136748-38136757
39	SPI1	chr17:38135961-38136423	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38083515..38085044-chr17:38134757..38136907,2	K562	blood:
2	chr17:38132843..38134558-chr17:38134586..38136777,2	K562	blood:
3	chr17:38073305..38078163-chr17:38135913..38140017,5	K562	blood:
4	chr17:37822499..37825157-chr17:38134564..38136982,2	K562	blood:
5	chr17:38115204..38116742-chr17:38135423..38136956,2	K562	blood:
6	chr17:38073305..38078633-chr17:38135671..38140017,6	K562	blood:
7	chr17:38063855..38068073-chr17:38135195..38137481,3	K562	blood:
8	chr17:38135295..38137617-chr17:38176453..38178456,2	K562	blood:

Variant related genes	Relation type
PSMD3	TF binding region
ENSG00000141744	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000073605	Chromatin interaction
ENSG00000264968	Chromatin interaction
ENSG00000172057	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11078930	0.95[ASN][1000 genomes]
rs11078931	0.93[ASN][1000 genomes]
rs11078935	0.80[ASN][1000 genomes]
rs11655264	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11658328	0.96[ASN][1000 genomes]
rs11867302	0.91[ASN][1000 genomes]
rs12309	0.86[ASN][1000 genomes]
rs12450800	0.94[ASN][1000 genomes]
rs12451547	0.87[ASN][1000 genomes]
rs12451897	0.87[ASN][1000 genomes]
rs12453334	0.95[ASN][1000 genomes]
rs12453341	0.87[ASN][1000 genomes]
rs12453343	0.87[ASN][1000 genomes]
rs12453764	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12602514	0.83[ASN][1000 genomes]
rs12940405	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2227319	0.88[ASN][1000 genomes]
rs2227321	0.88[ASN][1000 genomes]
rs2227333	0.88[ASN][1000 genomes]
rs2241244	0.96[ASN][1000 genomes]
rs2241245	0.96[ASN][1000 genomes]
rs2270401	0.88[ASN][1000 genomes]
rs2302774	0.87[ASN][1000 genomes]
rs2302777	0.87[ASN][1000 genomes]
rs2305481	0.96[ASN][1000 genomes]
rs2305482	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs25645	0.87[ASN][1000 genomes]
rs3087852	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34342173	0.89[ASN][1000 genomes]
rs34453912	0.86[ASN][1000 genomes]
rs34648856	0.94[ASN][1000 genomes]
rs34933056	0.89[ASN][1000 genomes]
rs35272691	0.90[ASN][1000 genomes]
rs36071767	0.83[ASN][1000 genomes]
rs3744245	0.94[ASN][1000 genomes]
rs3785550	0.93[ASN][1000 genomes]
rs3816472	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3859187	0.96[ASN][1000 genomes]
rs3859189	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3935281	0.82[ASN][1000 genomes]
rs4065321	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4072639	0.82[ASN][1000 genomes]
rs4433838	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7502971	0.84[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	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9915252	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9916158	0.87[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9898547	GSDMA	cis	Adipose Subcutaneous	GTEx
rs9898547	GSDMA	cis	Nerve Tibial	GTEx
rs9898547	GSDMA	cis	lung	GTEx
rs9898547	GSDMA	cis	Artery Aorta	GTEx
rs9898547	GSDMA	cis	Esophagus Muscularis	GTEx
rs9898547	MED24	cis	Artery Tibial	GTEx
rs9898547	GSDMA	cis	Artery Tibial	GTEx
rs9898547	MED24	cis	Nerve Tibial	GTEx
rs9898547	GSDMA	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38133000-38136200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:38134800-38136200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr17:38134800-38136200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:38135200-38136200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr17:38135200-38136200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr17:38135400-38136200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr17:38135400-38136200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr17:38135400-38136200	Enhancers	Fetal Thymus	thymus
9	chr17:38135400-38136400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:38135400-38136600	Flanking Active TSS	NH-A	brain
11	chr17:38135400-38136600	Flanking Active TSS	NHEK	skin
12	chr17:38135400-38137800	Active TSS	Duodenum Mucosa	Duodenum
13	chr17:38135600-38136200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr17:38135600-38136200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr17:38135600-38136200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr17:38135600-38136200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:38135600-38136200	Enhancers	Primary T cells from cord blood	blood
18	chr17:38135600-38136200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:38135600-38136200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr17:38135600-38136200	Enhancers	Colon Smooth Muscle	Colon
21	chr17:38135600-38136200	Bivalent Enhancer	Fetal Heart	heart
22	chr17:38135600-38136200	Enhancers	Placenta	Placenta
23	chr17:38135600-38136200	Enhancers	Thymus	Thymus
24	chr17:38135600-38136400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr17:38135600-38136400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr17:38135600-38136400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:38135600-38136400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr17:38135600-38136600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr17:38135600-38136600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:38135600-38136600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr17:38135600-38136600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr17:38135600-38136600	Flanking Active TSS	Osteobl	bone
33	chr17:38135600-38136800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr17:38135800-38136200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:38135800-38136200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr17:38135800-38136200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr17:38135800-38136200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr17:38135800-38136200	Enhancers	Primary T cells fromperipheralblood	blood
39	chr17:38135800-38136200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr17:38135800-38136200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr17:38135800-38136200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr17:38135800-38136200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:38135800-38136200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr17:38135800-38136200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr17:38135800-38136200	Enhancers	Liver	Liver
46	chr17:38135800-38136200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:38135800-38136200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr17:38135800-38136200	Enhancers	Fetal Kidney	kidney
49	chr17:38135800-38136200	Enhancers	Fetal Muscle Leg	muscle
50	chr17:38135800-38136200	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links