Variant report

Variant	rs1038392
Chromosome Location	chr3:47419076-47419077
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	POLR2A	chr3:47417906-47419271	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:47418721-47419135	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:47418734-47419160	HepG2	liver:	n/a	n/a
6	SPI1	chr3:47418681-47419144	HL-60	blood:	n/a	chr3:47418882-47418889 chr3:47418889-47418898 chr3:47418893-47418902 chr3:47418891-47418904
7	SPI1	chr3:47418761-47419121	HL-60	blood:	n/a	chr3:47418882-47418889 chr3:47418889-47418898 chr3:47418893-47418902 chr3:47418891-47418904
8	MTA3	chr3:47418626-47419122	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:47418720-47419111	HCT-116	colon:	n/a	n/a
10	POLR2A	chr3:47418568-47419140	GM12878	blood:	n/a	n/a
11	SPI1	chr3:47418672-47419093	GM12891	blood:	n/a	chr3:47418882-47418889 chr3:47418889-47418898 chr3:47418893-47418902 chr3:47418891-47418904
12	POLR2A	chr3:47417923-47419142	K562	blood:	n/a	n/a
13	POLR2A	chr3:47418852-47419187	K562	blood:	n/a	n/a
14	POLR2A	chr3:47418784-47419114	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:47418699-47419135	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47417993..47420029-chr3:47421038..47423395,2	MCF-7	breast:
2	chr3:47403977..47407169-chr3:47419054..47422081,3	K562	blood:
3	chr3:47412852..47414876-chr3:47416548..47419778,4	K562	blood:
4	chr3:47023369..47025258-chr3:47417930..47420658,2	MCF-7	breast:
5	chr3:47321814..47325452-chr3:47418885..47424380,8	K562	blood:

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

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12106745	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17079575	0.82[YRI][hapmap]
rs17079693	0.95[YRI][hapmap]
rs56398518	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59825859	0.89[AMR][1000 genomes]
rs6799812	0.82[YRI][hapmap]
rs6807733	0.83[YRI][hapmap]
rs6810322	1.00[YRI][hapmap]
rs72911242	0.81[AMR][1000 genomes]
rs72911269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72911287	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7642630	0.89[AMR][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:44 , 50 per page) page: 1

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	chr3:47418200-47419200	Enhancers	Pancreas	Pancrea
18	chr3:47418200-47419800	Strong transcription	Fetal Stomach	stomach
19	chr3:47418400-47419200	Enhancers	Primary B cells from cord blood	blood
20	chr3:47418400-47419200	Enhancers	Primary B cells from peripheral blood	blood
21	chr3:47418400-47419200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr3:47418400-47419400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:47418600-47419200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr3:47418600-47419200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:47418600-47419200	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr3:47418600-47419200	Enhancers	Placenta	Placenta
27	chr3:47418600-47419200	Enhancers	Lung	lung
28	chr3:47418600-47420400	Enhancers	GM12878-XiMat	blood
29	chr3:47418600-47421000	Weak transcription	Brain Anterior Caudate	brain
30	chr3:47418800-47419200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:47418800-47419200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:47418800-47419200	Enhancers	Liver	Liver
33	chr3:47418800-47419200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:47418800-47419200	Enhancers	Fetal Muscle Trunk	muscle
35	chr3:47418800-47421000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:47419000-47419200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:47419000-47419200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr3:47419000-47419200	Enhancers	Stomach Mucosa	stomach
39	chr3:47419000-47420600	Weak transcription	Brain Substantia Nigra	brain
40	chr3:47419000-47420600	Weak transcription	Thymus	Thymus
41	chr3:47419000-47420800	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:47419000-47421000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:47419000-47421000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:47419000-47421600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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