Variant report

Variant	rs1039351
Chromosome Location	chr3:20711563-20711564
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1392568	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1392569	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2886695	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2886696	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58750373	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7613234	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7615702	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9826159	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9852717	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv876598	chr3:20242143-20970042	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv876599	chr3:20264950-20813009	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv876603	chr3:20626326-20727885	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv460460	chr3:20638228-20718124	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
7	nsv589866	chr3:20638228-20718124	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1039351	C3orf48	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20708000-20711600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:20708200-20711600	Enhancers	NHDF-Ad	bronchial
3	chr3:20709400-20711600	Enhancers	Ovary	ovary
4	chr3:20709400-20711600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr3:20709400-20712400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr3:20709800-20711800	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:20710000-20711600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:20710000-20711600	Enhancers	Brain Substantia Nigra	brain
9	chr3:20710000-20711600	Enhancers	Fetal Muscle Leg	muscle
10	chr3:20710000-20711600	Enhancers	Left Ventricle	heart
11	chr3:20710000-20711600	Enhancers	Pancreas	Pancrea
12	chr3:20710000-20711600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:20710000-20711600	Enhancers	Stomach Smooth Muscle	stomach
14	chr3:20710000-20711800	Enhancers	Psoas Muscle	Psoas
15	chr3:20710200-20711600	Enhancers	Aorta	Aorta
16	chr3:20710800-20711600	Enhancers	HSMMtube	muscle
17	chr3:20711000-20711800	Enhancers	Brain Hippocampus Middle	brain
18	chr3:20711200-20711600	Enhancers	Fetal Brain Female	brain
19	chr3:20711400-20711800	Weak transcription	Fetal Brain Male	brain

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

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