Variant report

Variant	rs4795397
Chromosome Location	chr17:38023745-38023746
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	MEF2C	chr17:38023065-38024527	GM12878	blood:	n/a	chr17:38023410-38023431 chr17:38023488-38023496
2	POLR2A	chr17:38022336-38024945	GM18505	blood:	n/a	n/a
3	NFATC1	chr17:38023099-38024499	GM12878	blood:	n/a	n/a
4	BCL3	chr17:38023200-38024490	GM12878	blood:	n/a	chr17:38023905-38023914 chr17:38024227-38024236 chr17:38024411-38024424
5	BCLAF1	chr17:38023108-38024567	GM12878	blood:	n/a	chr17:38023905-38023914 chr17:38024227-38024236 chr17:38024411-38024424
6	TBL1XR1	chr17:38023178-38024491	GM12878	blood:	n/a	n/a
7	ATF2	chr17:38022555-38024496	GM12878	blood:	n/a	n/a
8	MXI1	chr17:38023234-38024276	GM12878	blood:	n/a	n/a
9	YY1	chr17:38023401-38024601	GM12878	blood:	n/a	chr17:38024411-38024420
10	NFATC1	chr17:38023054-38024330	GM12878	blood:	n/a	n/a
11	EBF1	chr17:38023283-38023786	GM12878	blood:	n/a	n/a
12	RELA	chr17:38023254-38024573	GM18951	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
13	BCL11A	chr17:38023373-38023765	GM12878	blood:	n/a	n/a
14	NFIC	chr17:38022926-38024693	GM12878	blood:	n/a	n/a
15	BHLHE40	chr17:38023169-38024618	GM12878	blood:	n/a	chr17:38024360-38024376 chr17:38024076-38024089 chr17:38024072-38024093
16	POLR2A	chr17:38023225-38024718	GM15510	blood:	n/a	n/a
17	WRNIP1	chr17:38023378-38024253	GM12878	blood:	n/a	n/a
18	RELA	chr17:38023169-38024357	GM12878	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
19	POLR2A	chr17:38023153-38024680	GM12891	blood:	n/a	n/a
20	STAT5A	chr17:38023077-38024790	GM12878	blood:	n/a	chr17:38024274-38024282 chr17:38024733-38024745 chr17:38024106-38024118
21	RELA	chr17:38023172-38024484	GM18505	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
22	MTA3	chr17:38022147-38025265	GM12878	blood:	n/a	n/a
23	IRF4	chr17:38023172-38024330	GM12878	blood:	n/a	chr17:38023493-38023507
24	PAX5	chr17:38023413-38024704	GM12878	blood:	n/a	n/a
25	PAX5	chr17:38023173-38024641	GM12878	blood:	n/a	n/a
26	RUNX3	chr17:38023032-38024461	GM12878	blood:	n/a	n/a
27	IKZF1	chr17:38023136-38024292	GM12878	blood:	n/a	n/a
28	POLR2A	chr17:38023065-38024781	GM12892	blood:	n/a	n/a
29	TBP	chr17:38023036-38024166	GM12878	blood:	n/a	n/a
30	RELA	chr17:38023213-38024514	GM15510	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
31	RELA	chr17:38023075-38024469	GM19193	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
32	POLR2A	chr17:38023143-38024679	GM12891	blood:	n/a	n/a
33	NFIC	chr17:38023081-38024487	GM12878	blood:	n/a	n/a
34	POLR2A	chr17:38023052-38024517	GM12878	blood:	n/a	n/a
35	MAX	chr17:38023337-38024660	GM12878	blood:	n/a	chr17:38024367-38024376
36	POLR2A	chr17:38023115-38024854	GM12892	blood:	n/a	n/a
37	BATF	chr17:38023205-38024346	GM12878	blood:	n/a	chr17:38023358-38023368
38	SP1	chr17:38023177-38024307	GM12878	blood:	n/a	n/a
39	POLR2A	chr17:38023137-38024880	GM12892	blood:	n/a	n/a
40	PAX5	chr17:38023409-38023793	GM12878	blood:	n/a	n/a
41	POLR2A	chr17:38023146-38024610	GM12891	blood:	n/a	n/a
42	MTA3	chr17:38023069-38024733	GM12878	blood:	n/a	n/a
43	EP300	chr17:38023278-38024310	GM12878	blood:	n/a	n/a
44	IRF4	chr17:38023157-38024339	GM12878	blood:	n/a	chr17:38023493-38023507
45	CEBPB	chr17:38022400-38024352	GM12878	blood:	n/a	n/a
46	POLR2A	chr17:38023125-38024730	GM19099	blood:	n/a	n/a
47	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
48	YY1	chr17:38023416-38024655	GM12892	blood:	n/a	chr17:38024411-38024420
49	STAT5A	chr17:38023157-38024589	GM12878	blood:	n/a	chr17:38024274-38024282 chr17:38024106-38024118
50	RELA	chr17:38023161-38024571	GM12892	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38016485..38022109-chr17:38022345..38027890,7	K562	blood:

Variant related genes	Relation type
ZPBP2	TF binding region
IKZF3	TF binding region
ENSG00000161405	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1008723	0.82[CEU][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];0.81[EUR][1000 genomes]
rs10852936	0.95[CEU][hapmap]
rs11078925	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078926	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078927	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078928	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11557466	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11557467	0.81[CEU][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11650661	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11651596	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11655198	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11655292	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11658993	0.82[EUR][1000 genomes]
rs11870965	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[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	0.90[ASN][1000 genomes]
rs12709365	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12936231	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12936409	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12939832	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12944882	0.84[ASN][1000 genomes]
rs12946510	0.95[CEU][hapmap]
rs12949100	0.84[AMR][1000 genomes];0.92[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	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1453559	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290400	0.81[CEU][hapmap];0.92[ASN][1000 genomes]
rs2305479	0.82[CEU][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305480	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2872516	0.91[ASN][1000 genomes]
rs34120102	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36000226	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3744246	0.81[ASN][1000 genomes]
rs3816470	0.82[CEU][hapmap];0.84[ASN][1000 genomes]
rs4065275	0.90[ASN][1000 genomes]
rs4794820	0.89[ASN][1000 genomes]
rs4795395	0.80[EUR][1000 genomes]
rs4795399	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795400	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795401	0.94[ASN][1000 genomes]
rs4795405	0.89[ASN][1000 genomes]
rs56380902	0.94[ASN][1000 genomes]
rs62067034	0.95[ASN][1000 genomes]
rs6503524	0.94[ASN][1000 genomes]
rs7216389	0.82[CEU][hapmap];0.94[ASN][1000 genomes]
rs7216558	0.94[ASN][1000 genomes]
rs7219923	0.82[CEU][hapmap];0.94[ASN][1000 genomes]
rs7221605	0.94[ASN][1000 genomes]
rs7224129	0.82[CEU][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];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8074437	0.92[ASN][1000 genomes]
rs8076131	0.91[CEU][hapmap];0.89[ASN][1000 genomes]
rs869402	0.82[CEU][hapmap];0.94[ASN][1000 genomes]
rs883770	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs907091	0.82[CEU][hapmap]
rs907092	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs921649	0.94[ASN][1000 genomes]
rs921650	0.94[ASN][1000 genomes]
rs9303277	0.82[CEU][hapmap]
rs9303279	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9303280	0.94[ASN][1000 genomes]
rs9303281	0.82[CEU][hapmap];0.94[ASN][1000 genomes]
rs9906951	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9909593	1.00[CEU][hapmap];0.82[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
rs4795397	IKZF3	cis	multi-tissue	Pritchard
rs4795397	ORMDL3	cis	Whole Blood	GTEx
rs4795397	GSDMB	cis	Whole Blood	GTEx
rs4795397	ORMDL3	cis	multi-tissue	Pritchard
rs4795397	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs4795397	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38020600-38024200	Weak transcription	Spleen	Spleen
2	chr17:38020800-38023800	Weak transcription	Pancreas	Pancrea
3	chr17:38021000-38024200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:38021400-38024200	Enhancers	Primary T cells from cord blood	blood
5	chr17:38021600-38024000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr17:38022200-38025200	Flanking Active TSS	GM12878-XiMat	blood
7	chr17:38022400-38025200	Enhancers	Primary B cells from cord blood	blood
8	chr17:38023200-38024000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr17:38023200-38024200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr17:38023200-38024400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr17:38023200-38024400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:38023200-38024600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr17:38023400-38024200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:38023400-38024400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
15	chr17:38023400-38024800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr17:38023400-38024800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr17:38023400-38024800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr17:38023600-38023800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:38023600-38023800	Bivalent Enhancer	Placenta	Placenta
20	chr17:38023600-38024000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:38023600-38024000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:38023600-38024200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
23	chr17:38023600-38024200	Bivalent Enhancer	Fetal Thymus	thymus
24	chr17:38023600-38024200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
25	chr17:38023600-38024800	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr17:38023600-38024800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:38023600-38025000	ZNF genes & repeats	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links