Variant report

Variant	rs6765381
Chromosome Location	chr3:54173258-54173259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12630117	0.90[CEU][hapmap]
rs1449336	0.95[CEU][hapmap]
rs4428220	0.87[AFR][1000 genomes]
rs4927998	0.90[CEU][hapmap]
rs4928001	0.95[CEU][hapmap]
rs4928004	0.95[CEU][hapmap]
rs6796475	0.82[CHD][hapmap]
rs6809942	0.95[CEU][hapmap];0.80[TSI][hapmap]
rs7623444	0.88[ASN][1000 genomes]
rs7639142	0.91[AFR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6765381	SPCS1	cis	cerebellum	SCAN
rs6765381	SPATA12	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54158200-54176200	Weak transcription	Ovary	ovary
2	chr3:54159800-54180400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:54160000-54180200	Weak transcription	Hela-S3	cervix
4	chr3:54165600-54173800	Weak transcription	Psoas Muscle	Psoas
5	chr3:54170800-54176800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:54170800-54180200	Weak transcription	Right Atrium	heart
7	chr3:54171200-54174600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:54171200-54176600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:54172800-54174600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:54173000-54173400	Enhancers	Liver	Liver
11	chr3:54173000-54174200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:54173000-54174800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:54173200-54173400	Enhancers	Right Ventricle	heart
14	chr3:54173200-54174000	Enhancers	Brain Anterior Caudate	brain

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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

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