Variant report

Variant	rs11557466
Chromosome Location	chr17:38024626-38024627
allele	C/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	POLR2A	chr17:38022336-38024945	GM18505	blood:	n/a	n/a
2	MAX	chr17:38024058-38024697	H1-hESC	embryonic stem cell:	n/a	chr17:38024367-38024376
3	NFIC	chr17:38022926-38024693	GM12878	blood:	n/a	n/a
4	E2F6	chr17:38024145-38024703	H1-hESC	embryonic stem cell:	n/a	chr17:38024313-38024327 chr17:38024316-38024323 chr17:38024341-38024348 chr17:38024316-38024323 chr17:38024316-38024323 chr17:38024341-38024348 chr17:38024341-38024348 chr17:38024312-38024324 chr17:38024340-38024349 chr17:38024411-38024420
5	POLR2A	chr17:38023225-38024718	GM15510	blood:	n/a	n/a
6	TCF3	chr17:38024201-38024647	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:38023153-38024680	GM12891	blood:	n/a	n/a
8	STAT5A	chr17:38023077-38024790	GM12878	blood:	n/a	chr17:38024274-38024282 chr17:38024733-38024745 chr17:38024106-38024118
9	MTA3	chr17:38022147-38025265	GM12878	blood:	n/a	n/a
10	PAX5	chr17:38023413-38024704	GM12878	blood:	n/a	n/a
11	PAX5	chr17:38023173-38024641	GM12878	blood:	n/a	n/a
12	POLR2A	chr17:38023065-38024781	GM12892	blood:	n/a	n/a
13	POLR2A	chr17:38023143-38024679	GM12891	blood:	n/a	n/a
14	MAX	chr17:38023337-38024660	GM12878	blood:	n/a	chr17:38024367-38024376
15	POLR2A	chr17:38023115-38024854	GM12892	blood:	n/a	n/a
16	CTCF	chr17:38024559-38024639	GM12892	blood:	n/a	n/a
17	POLR2A	chr17:38023137-38024880	GM12892	blood:	n/a	n/a
18	MTA3	chr17:38023069-38024733	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:38023125-38024730	GM19099	blood:	n/a	n/a
20	SP1	chr17:38023278-38024630	GM12878	blood:	n/a	chr17:38024410-38024420 chr17:38024410-38024419 chr17:38024410-38024420 chr17:38024409-38024421 chr17:38024411-38024420 chr17:38024409-38024421 chr17:38024410-38024419
21	YY1	chr17:38023416-38024655	GM12892	blood:	n/a	chr17:38024411-38024420
22	POLR2A	chr17:38023072-38024757	GM12878	blood:	n/a	n/a
23	POU2F2	chr17:38023359-38024731	GM12891	blood:	n/a	chr17:38023871-38023893
24	RELA	chr17:38023223-38024775	GM12891	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
25	TAF1	chr17:38024163-38024720	GM12892	blood:	n/a	n/a
26	POLR2A	chr17:38023072-38024892	GM12892	blood:	n/a	n/a
27	POLR2A	chr17:38023464-38024678	GM12878	blood:	n/a	n/a
28	POLR2A	chr17:38024573-38024683	A549	lung:	n/a	n/a
29	BCLAF1	chr17:38023174-38024636	GM12878	blood:	n/a	chr17:38023905-38023914 chr17:38024227-38024236 chr17:38024411-38024424
30	POLR2A	chr17:38023476-38024663	GM12878	blood:	n/a	n/a
31	FOXM1	chr17:38023055-38024668	GM12878	blood:	n/a	n/a
32	PAX5	chr17:38024143-38024630	GM12892	blood:	n/a	n/a
33	ELF1	chr17:38023925-38024981	GM12878	blood:	n/a	chr17:38024410-38024422
34	RCOR1	chr17:38023279-38024780	GM12878	blood:	n/a	n/a
35	E2F6	chr17:38023670-38024740	H1-hESC	embryonic stem cell:	n/a	chr17:38024313-38024327 chr17:38024316-38024323 chr17:38024341-38024348 chr17:38024316-38024323 chr17:38024316-38024323 chr17:38024341-38024348 chr17:38024341-38024348 chr17:38024312-38024324 chr17:38024340-38024349 chr17:38024411-38024420
36	PML	chr17:38023019-38024702	GM12878	blood:	n/a	n/a
37	RELA	chr17:38023232-38024677	GM19099	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
38	RUNX3	chr17:38023179-38024948	GM12878	blood:	n/a	n/a
39	POLR2A	chr17:38023089-38024884	GM12892	blood:	n/a	n/a
40	FOXM1	chr17:38022987-38024705	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:

Variant related genes	Relation type
IKZF3	TF binding region
ENSG00000161405	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1008723	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1011082	0.94[ASN][1000 genomes]
rs1031458	0.94[ASN][1000 genomes]
rs1031460	0.94[ASN][1000 genomes]
rs10445308	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs10852936	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11078921	0.81[CHB][hapmap]
rs11078925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078928	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11557467	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11650661	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11651596	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11655198	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11655292	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11870965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12103884	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12453507	0.86[ASN][1000 genomes]
rs12603332	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12709365	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12936231	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12936409	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12939832	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12944882	0.84[ASN][1000 genomes]
rs12946510	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs12949100	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12950209	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12950743	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13380815	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1453559	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290400	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2305479	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2872516	0.91[ASN][1000 genomes]
rs34120102	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36000226	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3744246	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs3816470	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4065275	0.90[ASN][1000 genomes]
rs4794820	0.90[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4795397	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795399	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795401	0.94[ASN][1000 genomes]
rs4795402	0.82[JPT][hapmap]
rs4795403	0.82[JPT][hapmap]
rs4795404	0.82[JPT][hapmap]
rs4795405	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs56380902	0.94[ASN][1000 genomes]
rs62067034	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6503524	0.94[ASN][1000 genomes]
rs7216389	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7216558	0.94[ASN][1000 genomes]
rs7219923	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7221605	0.94[ASN][1000 genomes]
rs7221814	0.81[AMR][1000 genomes]
rs7224129	0.83[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs7359623	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8065777	0.94[ASN][1000 genomes]
rs8067378	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8069176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8074437	0.92[ASN][1000 genomes]
rs8076131	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs869402	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs883770	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs907091	0.90[CHB][hapmap]
rs907092	0.95[CEU][hapmap]
rs921649	0.94[ASN][1000 genomes]
rs921650	0.94[ASN][1000 genomes]
rs9303277	0.83[CEU][hapmap];0.95[CHB][hapmap]
rs9303279	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9303280	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs9303281	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9635726	0.86[CHB][hapmap]
rs9906951	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9909593	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[EUR][1000 genomes]
rs9916765	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11557466	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs11557466	GSDMB	cis	Whole Blood	GTEx
rs11557466	ORMDL3	cis	multi-tissue	Pritchard
rs11557466	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs11557466	IKZF3	cis	multi-tissue	Pritchard
rs11557466	ORMDL3	cis	Whole Blood	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38022200-38025200	Flanking Active TSS	GM12878-XiMat	blood
2	chr17:38022400-38025200	Enhancers	Primary B cells from cord blood	blood
3	chr17:38023400-38024800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr17:38023400-38024800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr17:38023400-38024800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr17:38023600-38024800	Flanking Active TSS	Primary B cells from peripheral blood	blood
7	chr17:38023600-38024800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:38023600-38025000	ZNF genes & repeats	Esophagus	oesophagus
9	chr17:38024000-38024800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:38024200-38024800	ZNF genes & repeats	Spleen	Spleen
11	chr17:38024200-38025000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:38024400-38024800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr17:38024400-38024800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:38024400-38025000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:38024400-38025000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr17:38024600-38024800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr17:38024600-38024800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr17:38024600-38024800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:38024600-38024800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr17:38024600-38024800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:38024600-38024800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr17:38024600-38024800	Bivalent Enhancer	Fetal Intestine Large	intestine
23	chr17:38024600-38025000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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