Variant report

Variant	rs9840476
Chromosome Location	chr3:50711758-50711759
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	MAX	chr3:50711562-50713165	H1-hESC	embryonic stem cell:	n/a	chr3:50712815-50712825 chr3:50712930-50712940 chr3:50713023-50713032
2	MAX	chr3:50711582-50713112	H1-hESC	embryonic stem cell:	n/a	chr3:50712815-50712825 chr3:50712930-50712940 chr3:50713023-50713032
3	ZNF263	chr3:50710949-50712130	HEK293-T-REx	kidney:	n/a	n/a
4	E2F6	chr3:50711553-50712665	H1-hESC	embryonic stem cell:	n/a	chr3:50712579-50712588 chr3:50712471-50712480 chr3:50712337-50712346
5	BACH1	chr3:50711747-50713161	H1-hESC	embryonic stem cell:	n/a	n/a
6	SPI1	chr3:50711275-50711820	HL-60	blood:	n/a	chr3:50711559-50711568
7	SPI1	chr3:50711302-50711775	HL-60	blood:	n/a	chr3:50711559-50711568
8	KAP1	chr3:50711115-50712120	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
DOCK3	TF binding region
MIR4787	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1038415	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs107457	0.83[ASW][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130258	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11923336	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13092850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13325937	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1552255	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1552256	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051012	1.00[EUR][1000 genomes]
rs17051016	1.00[EUR][1000 genomes]
rs17051017	1.00[EUR][1000 genomes]
rs17051404	1.00[EUR][1000 genomes]
rs1843073	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2129069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2232251	1.00[EUR][1000 genomes]
rs2262848	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2355337	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2355701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2459450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2608994	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2608996	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2609004	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2609014	1.00[AMR][1000 genomes]
rs2609015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2609027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2609030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675775	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2675779	0.91[ASW][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap]
rs2675781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675797	1.00[AMR][1000 genomes]
rs2675798	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2675815	0.91[ASW][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs2675823	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675824	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675826	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675833	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs407164	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs421689	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234694	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234695	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4267639	0.82[ASW][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4340700	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4401355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4423762	1.00[AMR][1000 genomes]
rs4440121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4688675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4688704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4688717	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55852678	1.00[EUR][1000 genomes]
rs56112107	1.00[EUR][1000 genomes]
rs56198179	1.00[EUR][1000 genomes]
rs56341000	1.00[EUR][1000 genomes]
rs56413944	1.00[EUR][1000 genomes]
rs57756789	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57987466	1.00[EUR][1000 genomes]
rs58854038	1.00[EUR][1000 genomes]
rs58911362	1.00[EUR][1000 genomes]
rs59065723	1.00[EUR][1000 genomes]
rs59337835	1.00[EUR][1000 genomes]
rs59340349	1.00[EUR][1000 genomes]
rs59749820	1.00[EUR][1000 genomes]
rs59944295	1.00[EUR][1000 genomes]
rs60132317	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60209025	1.00[EUR][1000 genomes]
rs60455882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs609678	1.00[EUR][1000 genomes]
rs61032466	1.00[EUR][1000 genomes]
rs61455710	1.00[EUR][1000 genomes]
rs621975	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs628865	1.00[ASW][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446223	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs650473	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs665943	1.00[EUR][1000 genomes]
rs6768539	1.00[EUR][1000 genomes]
rs6789552	1.00[EUR][1000 genomes]
rs6807662	1.00[AMR][1000 genomes]
rs7373700	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833231	1.00[EUR][1000 genomes]
rs73833232	1.00[EUR][1000 genomes]
rs73833239	1.00[EUR][1000 genomes]
rs73833247	1.00[EUR][1000 genomes]
rs73833251	1.00[AMR][1000 genomes]
rs73833935	1.00[EUR][1000 genomes]
rs73833947	1.00[EUR][1000 genomes]
rs73833949	1.00[EUR][1000 genomes]
rs73833952	1.00[EUR][1000 genomes]
rs73835518	1.00[EUR][1000 genomes]
rs73835533	1.00[EUR][1000 genomes]
rs73835535	1.00[EUR][1000 genomes]
rs73835537	1.00[EUR][1000 genomes]
rs73835538	1.00[EUR][1000 genomes]
rs7611428	0.82[LWK][hapmap]
rs7642578	1.00[EUR][1000 genomes]
rs7650772	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652715	0.83[LWK][hapmap]
rs7653228	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936714	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9825283	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9851304	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854588	1.00[AMR][1000 genomes]
rs9857033	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	esv3398465	chr3:50710948-50713996	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9840476	PRPF6	trans	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50687000-50712000	Weak transcription	Right Atrium	heart
2	chr3:50709000-50711800	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:50709000-50711800	Weak transcription	Esophagus	oesophagus
4	chr3:50709400-50711800	Weak transcription	HSMMtube	muscle
5	chr3:50710200-50711800	Weak transcription	HSMM	muscle
6	chr3:50711400-50711800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:50711400-50711800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:50711400-50711800	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:50711400-50711800	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr3:50711400-50712000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:50711400-50712000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
12	chr3:50711400-50712000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
13	chr3:50711400-50712000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
14	chr3:50711400-50712200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:50711400-50714000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:50711400-50714400	Active TSS	Brain Angular Gyrus	brain
17	chr3:50711400-50714400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:50711600-50711800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
19	chr3:50711600-50711800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:50711600-50711800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:50711600-50711800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:50711600-50711800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr3:50711600-50711800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:50711600-50711800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:50711600-50711800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:50711600-50711800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:50711600-50711800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr3:50711600-50711800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
29	chr3:50711600-50711800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:50711600-50711800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:50711600-50711800	Weak transcription	Brain Anterior Caudate	brain
32	chr3:50711600-50711800	Weak transcription	Brain Substantia Nigra	brain
33	chr3:50711600-50711800	Active TSS	Rectal Smooth Muscle	rectum
34	chr3:50711600-50711800	Active TSS	Stomach Smooth Muscle	stomach
35	chr3:50711600-50711800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
36	chr3:50711600-50712000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr3:50711600-50712000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:50711600-50712000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr3:50711600-50712000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
40	chr3:50711600-50712000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:50711600-50712000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:50711600-50712000	Flanking Active TSS	Fetal Brain Female	brain
43	chr3:50711600-50712000	Bivalent Enhancer	Fetal Thymus	thymus
44	chr3:50711600-50712000	Enhancers	Pancreas	Pancrea
45	chr3:50711600-50712000	Enhancers	Right Ventricle	heart
46	chr3:50711600-50712000	Bivalent Enhancer	NH-A	brain
47	chr3:50711600-50712200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr3:50711600-50712200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
49	chr3:50711600-50712200	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr3:50711600-50712200	Bivalent Enhancer	Lung	lung

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