Variant report

Variant	rs12316771
Chromosome Location	chr12:117879236-117879237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10507280	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10850827	0.85[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11068499	0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[MKK][hapmap];0.87[YRI][hapmap]
rs11068500	0.90[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12302697	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12311157	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12312120	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12320449	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17618096	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34731287	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41279104	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900623	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560386	chr12:117822187-117991547	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv528231	chr12:117877110-117879236	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12316771	RFC5	cis	parietal	SCAN
rs12316771	SUDS3	cis	parietal	SCAN
rs12316771	RAD9B	trans	parietal	SCAN
rs12316771	NOS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117874400-117880400	Enhancers	Fetal Muscle Leg	muscle
2	chr12:117876600-117879600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:117877400-117888200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:117877800-117879400	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:117877800-117879600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:117878000-117879600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:117878600-117880000	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr12:117878600-117885800	Weak transcription	Pancreas	Pancrea
9	chr12:117878800-117879600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr12:117879200-117879600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:117879200-117879600	Enhancers	HSMM	muscle
12	chr12:117879200-117880000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:117879200-117880000	Enhancers	Brain Anterior Caudate	brain
14	chr12:117879200-117880000	Enhancers	A549	lung

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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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