Variant report

Variant	rs759306
Chromosome Location	chr12:4228941-4228942
allele	A/C
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	TBL1XR1	chr12:4227005-4228962	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:4223920-4228953	GM12878	blood:	n/a	n/a
3	IRF4	chr12:4227870-4229011	GM12878	blood:	n/a	n/a
4	CHD1	chr12:4226563-4229101	GM12878	blood:	n/a	n/a
5	ATF2	chr12:4227986-4228978	GM12878	blood:	n/a	n/a
6	CEBPB	chr12:4228152-4229019	GM12878	blood:	n/a	n/a
7	NFATC1	chr12:4228116-4229050	GM12878	blood:	n/a	n/a
8	ZNF143	chr12:4228073-4228965	GM12878	blood:	n/a	n/a
9	BATF	chr12:4228185-4228976	GM12878	blood:	n/a	n/a
10	NFIC	chr12:4227964-4229016	GM12878	blood:	n/a	n/a
11	RELA	chr12:4226135-4228945	GM12891	blood:	n/a	chr12:4226252-4226261 chr12:4226252-4226261
12	FOXM1	chr12:4227995-4228958	GM12878	blood:	n/a	n/a
13	RUNX3	chr12:4226837-4228951	GM12878	blood:	n/a	n/a
14	RUNX3	chr12:4226752-4229005	GM12878	blood:	n/a	n/a
15	NFATC1	chr12:4228187-4228959	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:4226455-4229144	GM12892	blood:	n/a	n/a
17	MTA3	chr12:4226774-4228984	GM12878	blood:	n/a	n/a
18	RELA	chr12:4225460-4228954	GM18951	blood:	n/a	chr12:4226252-4226261 chr12:4226252-4226261
19	CREB1	chr12:4228069-4228957	GM12878	blood:	n/a	n/a
20	RELA	chr12:4226655-4228988	GM18505	blood:	n/a	n/a
21	RELA	chr12:4225852-4229001	GM15510	blood:	n/a	chr12:4226252-4226261 chr12:4226252-4226261
22	STAT5A	chr12:4227982-4229015	GM12878	blood:	n/a	chr12:4228299-4228310
23	YY1	chr12:4228267-4228953	GM12878	blood:	n/a	n/a
24	PAX5	chr12:4226848-4229011	GM12878	blood:	n/a	chr12:4227438-4227447 chr12:4226852-4226861
25	CHD2	chr12:4226538-4229008	GM12878	blood:	n/a	n/a
26	RELA	chr12:4225409-4229031	GM19193	blood:	n/a	chr12:4226252-4226261 chr12:4226252-4226261
27	PML	chr12:4227986-4228969	GM12878	blood:	n/a	n/a
28	POU2F2	chr12:4226860-4229026	GM12878	blood:	n/a	chr12:4227885-4227897
29	MTA3	chr12:4226655-4229017	GM12878	blood:	n/a	n/a
30	IKZF1	chr12:4226719-4228979	GM12878	blood:	n/a	n/a
31	BCL11A	chr12:4228130-4228948	GM12878	blood:	n/a	n/a
32	RCOR1	chr12:4226916-4229006	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PARP11-6	chr12:4228815-4229034	NONHSAT025943

Variant related genes	Relation type
ENSG00000242444	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10774193	0.85[EUR][1000 genomes]
rs10774197	0.84[EUR][1000 genomes]
rs10848976	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10848978	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10848979	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10848981	0.86[EUR][1000 genomes]
rs10848982	0.86[EUR][1000 genomes]
rs10848983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848984	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848985	0.84[EUR][1000 genomes]
rs11062989	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11062992	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11062999	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11063000	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11063002	0.86[EUR][1000 genomes]
rs11063003	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11063004	1.00[CHB][hapmap];1.00[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]
rs11063007	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11063008	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11063009	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12227531	0.83[AMR][1000 genomes]
rs12228949	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12229320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230013	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12231207	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12579541	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579556	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579813	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2003578	0.86[EUR][1000 genomes]
rs2003579	0.86[EUR][1000 genomes]
rs2072497	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2110592	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160160	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160161	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2358594	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2358836	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358837	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2540139	0.89[EUR][1000 genomes]
rs3889565	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4765762	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4765767	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4765769	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4766207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766208	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766209	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4766211	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58334161	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59428290	0.83[AMR][1000 genomes]
rs59759498	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59925288	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60789908	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61269540	0.88[AMR][1000 genomes]
rs6489518	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7136346	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7304518	0.87[ASN][1000 genomes]
rs741243	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs741244	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs741245	0.86[EUR][1000 genomes]
rs759312	0.86[EUR][1000 genomes]
rs7967520	0.83[EUR][1000 genomes]
rs7975418	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs873613	0.82[EUR][1000 genomes]
rs9634153	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1050474	chr12:4226760-4389238	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4224000-4229000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:4224000-4229000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:4224200-4230000	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:4224600-4229000	Flanking Active TSS	GM12878-XiMat	blood
5	chr12:4226400-4230800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:4227000-4229000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:4227200-4252000	Weak transcription	Pancreas	Pancrea
8	chr12:4227400-4231000	Enhancers	Fetal Muscle Trunk	muscle
9	chr12:4227600-4229600	Enhancers	HSMMtube	muscle
10	chr12:4227600-4230200	Enhancers	HSMM	muscle
11	chr12:4227800-4229000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr12:4227800-4229200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr12:4227800-4229600	Enhancers	Primary B cells from cord blood	blood
14	chr12:4227800-4231200	Enhancers	Primary hematopoietic stem cells	blood
15	chr12:4228000-4231400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr12:4228000-4231400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:4228400-4229000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr12:4228600-4229800	Weak transcription	Small Intestine	intestine
19	chr12:4228800-4229400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:4228800-4229400	Weak transcription	Fetal Thymus	thymus
21	chr12:4228800-4231200	Enhancers	Fetal Muscle Leg	muscle

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