Variant report

Variant	rs1038393
Chromosome Location	chr3:47419000-47419001
allele	C/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	POLR2A	chr3:47417646-47419968	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:47418351-47419243	SK-N-MC	brain:	n/a	n/a
3	ELK1	chr3:47418743-47419008	GM12878	blood:	n/a	n/a
4	SPI1	chr3:47418728-47419064	GM12891	blood:	n/a	chr3:47418882-47418889 chr3:47418889-47418898 chr3:47418893-47418902 chr3:47418891-47418904
5	SRF	chr3:47418707-47419017	K562	blood:	n/a	n/a
6	POLR2A	chr3:47417906-47419271	MCF10A-Er-Src	breast:	n/a	n/a
7	ELF1	chr3:47418685-47419054	K562	blood:	n/a	chr3:47418893-47418904 chr3:47418891-47418904
8	POLR2A	chr3:47418721-47419135	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr3:47418734-47419160	HepG2	liver:	n/a	n/a
10	SPI1	chr3:47418681-47419144	HL-60	blood:	n/a	chr3:47418882-47418889 chr3:47418889-47418898 chr3:47418893-47418902 chr3:47418891-47418904
11	SPI1	chr3:47418726-47419028	GM12878	blood:	n/a	chr3:47418882-47418889 chr3:47418889-47418898 chr3:47418893-47418902 chr3:47418891-47418904
12	SPI1	chr3:47418761-47419121	HL-60	blood:	n/a	chr3:47418882-47418889 chr3:47418889-47418898 chr3:47418893-47418902 chr3:47418891-47418904
13	MTA3	chr3:47418626-47419122	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:47418448-47419043	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr3:47418720-47419111	HCT-116	colon:	n/a	n/a
16	POLR2A	chr3:47418568-47419140	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:47418795-47419004	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr3:47417903-47419071	Hela-S3	cervix:	n/a	n/a
19	SPI1	chr3:47418672-47419093	GM12891	blood:	n/a	chr3:47418882-47418889 chr3:47418889-47418898 chr3:47418893-47418902 chr3:47418891-47418904
20	SRF	chr3:47418744-47419013	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:47417923-47419142	K562	blood:	n/a	n/a
22	POLR2A	chr3:47418852-47419187	K562	blood:	n/a	n/a
23	POLR2A	chr3:47418784-47419114	HepG2	liver:	n/a	n/a
24	SRF	chr3:47418677-47419001	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:47418649-47419046	K562	blood:	n/a	n/a
26	POLR2A	chr3:47418699-47419135	Raji	blood:	n/a	n/a
27	POLR2A	chr3:47418576-47419046	PANC-1	pancreas:	n/a	n/a
28	MYC	chr3:47418943-47419021	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47417993..47420029-chr3:47421038..47423395,2	MCF-7	breast:
2	chr3:47412852..47414876-chr3:47416548..47419778,4	K562	blood:
3	chr3:47023369..47025258-chr3:47417930..47420658,2	MCF-7	breast:
4	chr3:47321814..47325452-chr3:47418885..47424380,8	K562	blood:

Variant related genes	Relation type
PTPN23	TF binding region
ENSG00000076201	Chromatin interaction
ENSG00000160799	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000114648	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1024036	1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs10865947	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1091068	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130134	0.89[AMR][1000 genomes]
rs11707272	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12631697	1.00[EUR][1000 genomes]
rs13077134	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1531874	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1872165	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2170814	0.87[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs295431	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4018904	1.00[EUR][1000 genomes]
rs448018	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858812	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858823	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858834	0.89[AMR][1000 genomes]
rs4858855	0.87[AMR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6442066	1.00[EUR][1000 genomes]
rs6442068	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs648226	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6772449	1.00[EUR][1000 genomes]
rs6778673	1.00[EUR][1000 genomes]
rs6778687	1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787210	1.00[EUR][1000 genomes]
rs6788978	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789730	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs7372780	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621853	1.00[AMR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7639121	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7649413	1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs807930	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs900688	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900689	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900690	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900694	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs924009	1.00[EUR][1000 genomes]
rs9819475	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9827293	1.00[EUR][1000 genomes]
rs9828124	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv3802	chr3:47396674-47441951	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47401600-47421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:47413200-47420200	Weak transcription	Spleen	Spleen
3	chr3:47413200-47420400	Weak transcription	Fetal Intestine Large	intestine
4	chr3:47413200-47420600	Weak transcription	Adipose Nuclei	Adipose
5	chr3:47413400-47420400	Weak transcription	Fetal Intestine Small	intestine
6	chr3:47413400-47420800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:47413600-47421000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:47414200-47421000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:47416200-47420800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:47417200-47420200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:47417600-47420600	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:47417600-47421000	Weak transcription	NHLF	lung
13	chr3:47417800-47420400	Enhancers	HepG2	liver
14	chr3:47418000-47419800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:47418000-47420600	Enhancers	K562	blood
16	chr3:47418000-47421600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr3:47418200-47419000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:47418200-47419200	Enhancers	Pancreas	Pancrea
19	chr3:47418200-47419800	Strong transcription	Fetal Stomach	stomach
20	chr3:47418400-47419200	Enhancers	Primary B cells from cord blood	blood
21	chr3:47418400-47419200	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:47418400-47419200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr3:47418400-47419400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:47418600-47419000	Enhancers	Brain Substantia Nigra	brain
25	chr3:47418600-47419000	Enhancers	Fetal Muscle Leg	muscle
26	chr3:47418600-47419000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:47418600-47419200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr3:47418600-47419200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:47418600-47419200	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr3:47418600-47419200	Enhancers	Placenta	Placenta
31	chr3:47418600-47419200	Enhancers	Lung	lung
32	chr3:47418600-47420400	Enhancers	GM12878-XiMat	blood
33	chr3:47418600-47421000	Weak transcription	Brain Anterior Caudate	brain
34	chr3:47418800-47419000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:47418800-47419000	Enhancers	Brain Angular Gyrus	brain
36	chr3:47418800-47419000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr3:47418800-47419000	Enhancers	Esophagus	oesophagus
38	chr3:47418800-47419000	Enhancers	Left Ventricle	heart
39	chr3:47418800-47419000	Enhancers	Right Ventricle	heart
40	chr3:47418800-47419000	Enhancers	Thymus	Thymus
41	chr3:47418800-47419200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr3:47418800-47419200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:47418800-47419200	Enhancers	Liver	Liver
44	chr3:47418800-47419200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr3:47418800-47419200	Enhancers	Fetal Muscle Trunk	muscle
46	chr3:47418800-47421000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:47419000-47419200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:47419000-47419200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr3:47419000-47419200	Enhancers	Stomach Mucosa	stomach
50	chr3:47419000-47420600	Weak transcription	Brain Substantia Nigra	brain

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