Variant report

Variant	rs1453559
Chromosome Location	chr17:38020419-38020420
allele	A/G
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	CHD2	chr17:38020346-38020578	K562	blood:	n/a	chr17:38020481-38020491
2	TAF7	chr17:38020333-38020664	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr17:38019552-38022062	GM12891	blood:	n/a	n/a
4	RAD21	chr17:38020286-38020783	HepG2	liver:	n/a	n/a
5	TCF12	chr17:38020295-38020641	GM12878	blood:	n/a	chr17:38020462-38020469
6	CTCF	chr17:38020287-38020780	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP4	chr17:38020305-38020671	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr17:38020280-38020620	SK-N-SH	brain:	n/a	chr17:38020427-38020437
9	RELA	chr17:38019794-38020816	GM18951	blood:	n/a	n/a
10	RAD21	chr17:38020333-38020743	GM12878	blood:	n/a	n/a
11	MAX	chr17:38020069-38020779	HCT-116	colon:	n/a	chr17:38020427-38020437
12	TCF12	chr17:38020051-38020726	A549	lung:	n/a	chr17:38020462-38020469
13	USF2	chr17:38020337-38020576	H1-hESC	embryonic stem cell:	n/a	chr17:38020503-38020519
14	MAZ	chr17:38020411-38020681	HepG2	liver:	n/a	n/a
15	ELF1	chr17:38020273-38020694	GM12878	blood:	n/a	n/a
16	MXI1	chr17:38020319-38020649	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr17:38020180-38020735	GM12892	blood:	n/a	chr17:38020504-38020518
18	CREB1	chr17:38020156-38020904	GM12878	blood:	n/a	n/a
19	PAX5	chr17:38020264-38020709	GM12878	blood:	n/a	n/a
20	STAT3	chr17:38020351-38021998	GM12878	blood:	n/a	n/a
21	RAD21	chr17:38020234-38020838	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr17:38020385-38020743	K562	blood:	n/a	n/a
23	MAX	chr17:38020181-38020666	K562	blood:	n/a	chr17:38020427-38020437
24	CTCF	chr17:38020338-38020743	HepG2	liver:	n/a	n/a
25	MAX	chr17:38020185-38020732	ECC-1	luminal epithelium:	n/a	chr17:38020427-38020437
26	KAP1	chr17:38020203-38020784	HEK293	kidney:	n/a	n/a
27	BHLHE40	chr17:38020320-38020646	K562	blood:	n/a	chr17:38020503-38020519
28	SRF	chr17:38020332-38020627	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr17:38020319-38020758	A549	lung:	n/a	n/a
30	YY1	chr17:38020213-38020606	K562	blood:	n/a	chr17:38020504-38020518
31	MAX	chr17:38020255-38020636	K562	blood:	n/a	chr17:38020427-38020437
32	ZEB1	chr17:38020297-38020683	GM12878	blood:	n/a	n/a
33	POLR2A	chr17:38019648-38022019	GM18505	blood:	n/a	n/a
34	CTCF	chr17:38020351-38020808	GM12878	blood:	n/a	n/a
35	POLR2A	chr17:38019769-38021967	GM18951	blood:	n/a	n/a
36	POLR2A	chr17:38020221-38020738	GM12878	blood:	n/a	n/a
37	CHD2	chr17:38020305-38020626	H1-hESC	embryonic stem cell:	n/a	chr17:38020481-38020491
38	TAF1	chr17:38020164-38020750	GM12878	blood:	n/a	n/a
39	BCLAF1	chr17:38019864-38022044	GM12878	blood:	n/a	n/a
40	POLR2A	chr17:38020082-38020814	GM12891	blood:	n/a	n/a
41	SP1	chr17:38020272-38020718	H1-hESC	embryonic stem cell:	n/a	n/a
42	FOXA1	chr17:38020078-38020473	HepG2	liver:	n/a	chr17:38020244-38020259
43	STAT5A	chr17:38020095-38020737	GM12878	blood:	n/a	n/a
44	JUND	chr17:38020346-38020758	K562	blood:	n/a	chr17:38020739-38020748
45	ATF2	chr17:38020263-38020561	H1-hESC	embryonic stem cell:	n/a	n/a
46	RELA	chr17:38019691-38020937	GM12891	blood:	n/a	n/a
47	EP300	chr17:38020392-38020584	K562	blood:	n/a	chr17:38020455-38020471 chr17:38020547-38020563
48	POU2F2	chr17:38020305-38020738	GM12878	blood:	n/a	n/a
49	MAZ	chr17:38020018-38020867	GM12878	blood:	n/a	n/a
50	SIN3A	chr17:38020044-38020753	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38016485..38022109-chr17:38022345..38027890,7	K562	blood:
2	chr17:37893210..37895843-chr17:38018530..38020744,2	MCF-7	breast:

Variant related genes	Relation type
IKZF3	TF binding region
ZPBP2	TF binding region
ENSG00000141738	Chromatin interaction
ENSG00000186075	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1008723	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1011082	0.94[ASN][1000 genomes]
rs1031458	0.94[ASN][1000 genomes]
rs1031460	0.94[ASN][1000 genomes]
rs11078925	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078926	0.95[ASN][1000 genomes]
rs11078927	0.95[ASN][1000 genomes]
rs11078928	0.95[ASN][1000 genomes]
rs11557466	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11557467	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11650661	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11651596	0.94[ASN][1000 genomes]
rs11655198	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11655292	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11870965	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12103884	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12453507	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12603332	0.90[ASN][1000 genomes]
rs12709365	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12936231	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12936409	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12939832	0.94[ASN][1000 genomes]
rs12944882	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12949100	0.95[ASN][1000 genomes]
rs12950209	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12950743	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13380815	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290400	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305479	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305480	0.95[ASN][1000 genomes]
rs2313430	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2872516	0.91[ASN][1000 genomes]
rs2952140	0.81[EUR][1000 genomes]
rs34120102	0.95[ASN][1000 genomes]
rs36000226	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3744246	0.81[ASN][1000 genomes]
rs3816470	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4065275	0.90[ASN][1000 genomes]
rs4794820	0.89[ASN][1000 genomes]
rs4795397	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795399	0.95[ASN][1000 genomes]
rs4795400	0.94[ASN][1000 genomes]
rs4795401	0.94[ASN][1000 genomes]
rs4795405	0.89[ASN][1000 genomes]
rs56380902	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62067034	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6503524	0.94[ASN][1000 genomes]
rs7216389	0.94[ASN][1000 genomes]
rs7216558	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7219923	0.94[ASN][1000 genomes]
rs7221605	0.94[ASN][1000 genomes]
rs7224129	0.90[ASN][1000 genomes]
rs7359623	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8065777	0.94[ASN][1000 genomes]
rs8067378	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8069176	0.95[ASN][1000 genomes]
rs8074437	0.92[ASN][1000 genomes]
rs8076131	0.89[ASN][1000 genomes]
rs869402	0.94[ASN][1000 genomes]
rs883770	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs921649	0.94[ASN][1000 genomes]
rs921650	0.94[ASN][1000 genomes]
rs9303277	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9303279	0.94[ASN][1000 genomes]
rs9303280	0.94[ASN][1000 genomes]
rs9303281	0.94[ASN][1000 genomes]
rs9906951	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9916765	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv1795575	chr17:37974075-38041762	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1453559	ORMDL3	cis	multi-tissue	Pritchard
rs1453559	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs1453559	GSDMB	cis	Whole Blood	GTEx
rs1453559	GSDMA	cis	Adipose Subcutaneous	GTEx
rs1453559	IKZF3	cis	multi-tissue	Pritchard
rs1453559	ORMDL3	cis	Whole Blood	GTEx
rs1453559	GSDML	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38017400-38021000	Active TSS	Primary T killer memory cells from peripheral blood	blood
2	chr17:38017800-38020600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:38017800-38020800	Active TSS	Primary B cells from cord blood	blood
4	chr17:38017800-38021000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr17:38017800-38021400	Active TSS	Primary B cells from peripheral blood	blood
6	chr17:38017800-38021400	Active TSS	Primary T cells fromperipheralblood	blood
7	chr17:38017800-38021400	Active TSS	GM12878-XiMat	blood
8	chr17:38018000-38021000	Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr17:38018000-38021000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:38018200-38021000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr17:38019200-38020800	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr17:38019200-38021000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:38019200-38021000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr17:38019400-38020800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:38019600-38021200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:38019600-38021200	Active TSS	Thymus	Thymus
17	chr17:38019800-38020800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:38019800-38020800	Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr17:38019800-38020800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
20	chr17:38019800-38020800	Bivalent/Poised TSS	Small Intestine	intestine
21	chr17:38020000-38020600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:38020000-38020600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
23	chr17:38020000-38020600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
24	chr17:38020000-38020600	Bivalent/Poised TSS	Colonic Mucosa	Colon
25	chr17:38020000-38020800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr17:38020000-38020800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:38020000-38020800	Bivalent/Poised TSS	Esophagus	oesophagus
28	chr17:38020000-38020800	Bivalent Enhancer	Fetal Intestine Large	intestine
29	chr17:38020000-38020800	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr17:38020000-38020800	Flanking Bivalent TSS/Enh	Sigmoid Colon	Sigmoid Colon
31	chr17:38020000-38020800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
32	chr17:38020000-38021000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
33	chr17:38020000-38021400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr17:38020200-38020600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:38020200-38020600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
36	chr17:38020200-38020600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr17:38020200-38020600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr17:38020200-38020600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:38020200-38020600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:38020200-38020600	Active TSS	Spleen	Spleen
41	chr17:38020200-38020800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:38020200-38020800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr17:38020200-38020800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
44	chr17:38020200-38020800	Active TSS	Primary T cells from cord blood	blood
45	chr17:38020200-38020800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
46	chr17:38020200-38020800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr17:38020200-38020800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr17:38020200-38020800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr17:38020200-38020800	Bivalent Enhancer	Fetal Intestine Small	intestine
50	chr17:38020200-38020800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links