Variant report

Variant	rs2670295
Chromosome Location	chr3:119315270-119315271
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	MTA3	chr3:119314705-119315717	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:119315222-119315664	GM12892	blood:	n/a	n/a
3	EP300	chr3:119315008-119315494	GM12878	blood:	n/a	chr3:119315433-119315447
4	POLR2A	chr3:119315198-119315664	GM12891	blood:	n/a	n/a
5	RUNX3	chr3:119314839-119315660	GM12878	blood:	n/a	n/a
6	STAT1	chr3:119314997-119315389	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:119314786-119315732	GM12892	blood:	n/a	n/a
8	CCNT2	chr3:119315181-119315511	K562	blood:	n/a	n/a
9	PML	chr3:119314495-119320501	GM12878	blood:	n/a	n/a
10	NFIC	chr3:119314902-119315655	GM12878	blood:	n/a	n/a
11	BHLHE40	chr3:119314957-119315629	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:119315265-119315740	GM12892	blood:	n/a	n/a
13	ZNF143	chr3:119314861-119315475	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:119314781-119315682	GM12891	blood:	n/a	n/a
15	POLR2A	chr3:119314772-119320568	GM12878	blood:	n/a	n/a
16	TBP	chr3:119314893-119315563	GM12878	blood:	n/a	n/a
17	FOXM1	chr3:119314957-119315720	GM12878	blood:	n/a	n/a
18	SMC3	chr3:119315015-119315554	GM12878	blood:	n/a	chr3:119315411-119315425

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119314543..119316146-chr3:119316320..119318446,2	K562	blood:
2	chr3:119310790..119313134-chr3:119314484..119316186,2	K562	blood:

Variant related genes	Relation type
PLA1A	TF binding region
ENSG00000144837	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1032131	0.84[EUR][1000 genomes]
rs1032132	0.84[EUR][1000 genomes]
rs12631518	0.84[EUR][1000 genomes]
rs12638684	0.84[EUR][1000 genomes]
rs12639410	0.84[EUR][1000 genomes]
rs13062086	0.84[EUR][1000 genomes]
rs13318540	0.84[EUR][1000 genomes]
rs1471792	0.84[EUR][1000 genomes]
rs1471793	0.84[EUR][1000 genomes]
rs1877595	0.84[EUR][1000 genomes]
rs1967051	0.84[EUR][1000 genomes]
rs1967052	0.84[EUR][1000 genomes]
rs2247660	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2280669	0.84[EUR][1000 genomes]
rs2629406	0.81[CEU][hapmap]
rs2670288	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3755583	0.84[EUR][1000 genomes]
rs3772132	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4688020	0.84[EUR][1000 genomes]
rs483349	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6799965	0.84[EUR][1000 genomes]
rs6800119	0.81[EUR][1000 genomes]
rs9832300	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs9834422	0.86[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv3963	chr3:119301064-119345904	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119299800-119318000	Weak transcription	Fetal Heart	heart
2	chr3:119306000-119316800	Weak transcription	Pancreas	Pancrea
3	chr3:119307600-119316400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:119310600-119319800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:119311000-119317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:119311200-119316800	Weak transcription	Fetal Lung	lung
7	chr3:119314200-119315400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:119314200-119315600	Enhancers	Right Ventricle	heart
9	chr3:119314200-119315600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr3:119314200-119317200	Enhancers	Lung	lung
11	chr3:119314400-119315400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:119314400-119315600	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr3:119314400-119318600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:119314600-119315400	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr3:119314600-119315400	Flanking Active TSS	GM12878-XiMat	blood
16	chr3:119314600-119315600	Enhancers	Primary hematopoietic stem cells	blood
17	chr3:119314600-119315600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:119314600-119315600	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:119314600-119315600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr3:119314600-119316200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:119314600-119316400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:119314800-119315400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:119314800-119315600	Enhancers	K562	blood
24	chr3:119314800-119315800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:119314800-119316200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:119314800-119316200	Enhancers	Placenta	Placenta
27	chr3:119314800-119316800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:119314800-119317400	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:119315000-119315400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:119315000-119315400	Enhancers	Small Intestine	intestine
31	chr3:119315000-119315400	Enhancers	NH-A	brain
32	chr3:119315000-119315600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr3:119315000-119315600	Enhancers	Gastric	stomach
34	chr3:119315000-119315800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:119315000-119315800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:119315000-119316200	Enhancers	Right Atrium	heart
37	chr3:119315000-119316200	Enhancers	Spleen	Spleen
38	chr3:119315000-119316400	Enhancers	Liver	Liver
39	chr3:119315000-119316400	Enhancers	Fetal Intestine Small	intestine
40	chr3:119315000-119316600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:119315000-119316800	Weak transcription	Ovary	ovary
42	chr3:119315000-119316800	Enhancers	HSMM	muscle
43	chr3:119315000-119317800	Enhancers	Adipose Nuclei	Adipose
44	chr3:119315000-119318000	Enhancers	Psoas Muscle	Psoas
45	chr3:119315000-119320200	Enhancers	Left Ventricle	heart
46	chr3:119315200-119315400	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:119315200-119315400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr3:119315200-119315400	Enhancers	Colon Smooth Muscle	Colon
49	chr3:119315200-119315400	Enhancers	NHDF-Ad	bronchial
50	chr3:119315200-119315600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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