Variant report

Variant	rs41292858
Chromosome Location	chr3:52548873-52548874
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52547472..52549650-chr3:52551017..52554363,3	K562	blood:

Variant related genes	Relation type
ENSG00000010327	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1011062	1.00[AFR][1000 genomes]
rs11721286	1.00[AFR][1000 genomes]
rs2109559	1.00[AFR][1000 genomes]
rs2335929	1.00[AFR][1000 genomes]
rs3774409	1.00[AFR][1000 genomes]
rs4312651	1.00[AFR][1000 genomes]
rs4687541	1.00[AFR][1000 genomes]
rs4687543	1.00[AFR][1000 genomes]
rs4687545	1.00[AFR][1000 genomes]
rs4687617	1.00[AFR][1000 genomes]
rs4687618	1.00[AFR][1000 genomes]
rs4687619	1.00[AFR][1000 genomes]
rs4687621	1.00[AFR][1000 genomes]
rs6414568	1.00[AFR][1000 genomes]
rs6445486	1.00[AFR][1000 genomes]
rs6445506	1.00[AFR][1000 genomes]
rs6771558	1.00[AFR][1000 genomes]
rs6782162	1.00[AFR][1000 genomes]
rs6810027	1.00[AFR][1000 genomes]
rs728408	1.00[AFR][1000 genomes]
rs758802	1.00[AFR][1000 genomes]
rs758803	1.00[AFR][1000 genomes]
rs7620015	1.00[AFR][1000 genomes]
rs9846089	1.00[AFR][1000 genomes]
rs9850471	1.00[AFR][1000 genomes]
rs9855470	1.00[AFR][1000 genomes]
rs9863753	1.00[AFR][1000 genomes]
rs9867823	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	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
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590306	chr3:52536308-52557440	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52530200-52551800	Weak transcription	Esophagus	oesophagus
2	chr3:52530400-52552400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:52530800-52551600	Weak transcription	Fetal Intestine Small	intestine
5	chr3:52533400-52549200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:52533400-52549200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:52533400-52558200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:52533400-52559800	Weak transcription	Liver	Liver
9	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:52536800-52552600	Strong transcription	Adipose Nuclei	Adipose
14	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:52540000-52553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:52540800-52549000	Weak transcription	Gastric	stomach
17	chr3:52542000-52557400	Weak transcription	Thymus	Thymus
18	chr3:52543800-52552000	Strong transcription	Lung	lung
19	chr3:52544000-52552400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:52544000-52557400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:52545200-52549000	Weak transcription	Placenta	Placenta
22	chr3:52545200-52552400	Weak transcription	Right Atrium	heart
23	chr3:52546800-52549800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:52547600-52552600	Weak transcription	Brain Anterior Caudate	brain
25	chr3:52547800-52550800	Weak transcription	HUVEC	blood vessel
26	chr3:52548200-52549400	Strong transcription	Colonic Mucosa	Colon
27	chr3:52548200-52549800	Enhancers	Right Ventricle	heart
28	chr3:52548400-52549200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:52548400-52549600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:52548400-52552400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:52548600-52549800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr3:52548600-52551000	Strong transcription	Spleen	Spleen
33	chr3:52548800-52549200	Flanking Bivalent TSS/Enh	HepG2	liver
34	chr3:52548800-52551000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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