Variant report

Variant	rs2053307
Chromosome Location	chr3:105174424-105174425
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1036581	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13100997	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2033802	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4894924	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6790159	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7428824	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7641185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288803	0.91[AFR][1000 genomes]
rs9827147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9827196	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9864062	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9870921	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105137400-105178600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:105144400-105185000	Weak transcription	Aorta	Aorta
3	chr3:105150800-105177800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:105155800-105177600	Weak transcription	HSMM	muscle
5	chr3:105163400-105177200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:105163600-105177400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:105167800-105174800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:105167800-105176600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:105167800-105177400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:105167800-105177400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:105167800-105185000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:105168000-105177800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:105168000-105178600	Weak transcription	A549	lung
14	chr3:105168200-105179400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:105169400-105174600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:105174400-105175400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr3:105174400-105175400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:105174400-105175800	Enhancers	Brain Hippocampus Middle	brain
19	chr3:105174400-105176000	Enhancers	Brain Angular Gyrus	brain

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links