Variant report

Variant	rs3774362
Chromosome Location	chr3:52853298-52853299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52847640..52851112-chr3:52852588..52855076,3	MCF-7	breast:
2	chr3:52737771..52740397-chr3:52851532..52853576,2	K562	blood:
3	chr3:52836954..52839305-chr3:52853241..52854782,2	K562	blood:

Variant related genes	Relation type
ENSG00000162267	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000055955	Chromatin interaction
ENSG00000016864	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11712498	1.00[YRI][hapmap]
rs17052501	1.00[AFR][1000 genomes]
rs17052546	1.00[AFR][1000 genomes]
rs17052574	1.00[AFR][1000 genomes]
rs17052577	0.91[AFR][1000 genomes]
rs1986467	0.85[AFR][1000 genomes]
rs2286797	0.80[AMR][1000 genomes]
rs34967967	1.00[AFR][1000 genomes]
rs35672271	1.00[AFR][1000 genomes]
rs4629327	0.89[AMR][1000 genomes]
rs58562470	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52844000-52854000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:52844200-52856600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:52844400-52857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:52844600-52856800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:52844600-52857600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:52845800-52854200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:52846400-52860800	Weak transcription	Esophagus	oesophagus
8	chr3:52846800-52857000	Weak transcription	Aorta	Aorta
9	chr3:52847000-52857400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:52847200-52861200	Genic enhancers	Liver	Liver
11	chr3:52847400-52857000	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
13	chr3:52847800-52854600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:52848400-52853400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:52848400-52865800	Weak transcription	Ovary	ovary
16	chr3:52848600-52853800	Weak transcription	Right Ventricle	heart
17	chr3:52848800-52854200	Weak transcription	Brain Substantia Nigra	brain
18	chr3:52849800-52853800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
20	chr3:52850600-52857800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:52850600-52864200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr3:52850800-52854000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:52850800-52865400	Strong transcription	Fetal Stomach	stomach
24	chr3:52851000-52856800	Weak transcription	Fetal Brain Female	brain
25	chr3:52851200-52855400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:52851600-52853800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:52851600-52863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:52851800-52853400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:52851800-52855200	Strong transcription	Brain Anterior Caudate	brain
30	chr3:52851800-52856800	Weak transcription	Lung	lung
31	chr3:52851800-52858000	Weak transcription	Placenta	Placenta
32	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:52852400-52853400	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:52852400-52853600	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr3:52852400-52854200	Genic enhancers	Fetal Thymus	thymus
36	chr3:52852400-52854400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr3:52852600-52853400	Genic enhancers	Spleen	Spleen
38	chr3:52852600-52854000	Weak transcription	Pancreas	Pancrea
39	chr3:52852800-52854800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
41	chr3:52853000-52853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:52853000-52854000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:52853000-52854400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr3:52853000-52854400	Strong transcription	Brain Germinal Matrix	brain
45	chr3:52853000-52857000	Weak transcription	Gastric	stomach
46	chr3:52853000-52857000	Enhancers	HepG2	liver
47	chr3:52853000-52857000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:52853000-52858400	Strong transcription	Brain Angular Gyrus	brain
49	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:52853200-52854000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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