Variant report

Variant	rs3128373
Chromosome Location	chr1:112858294-112858295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10857952	0.94[ASN][1000 genomes]
rs12127798	0.93[ASN][1000 genomes]
rs3124030	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3128364	0.81[ASN][1000 genomes]
rs3128365	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3128366	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3128367	0.93[JPT][hapmap]
rs3128371	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3128372	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4433390	0.93[ASN][1000 genomes]
rs5021965	0.94[ASN][1000 genomes]
rs7555668	0.90[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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv508526	chr1:112839396-112915215	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3128373	CEPT1	cis	cerebellum	SCAN
rs3128373	ARL9	trans	cerebellum	SCAN
rs3128373	NGF	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112851600-112866000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:112851800-112859400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:112853000-112860400	Weak transcription	Aorta	Aorta
4	chr1:112855600-112858800	Weak transcription	Fetal Lung	lung
5	chr1:112855600-112859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:112855600-112859200	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:112855800-112859800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:112856400-112859200	Weak transcription	HSMMtube	muscle
9	chr1:112856400-112863200	Enhancers	Adipose Nuclei	Adipose
10	chr1:112856600-112859400	Weak transcription	Ovary	ovary
11	chr1:112856800-112858800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:112857200-112858800	Weak transcription	Fetal Muscle Leg	muscle

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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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