Variant report

Variant	rs7555668
Chromosome Location	chr1:112856570-112856571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10857952	0.91[ASN][1000 genomes]
rs12127798	0.90[ASN][1000 genomes]
rs3124030	0.97[ASN][1000 genomes]
rs3128365	0.86[JPT][hapmap]
rs3128366	0.86[JPT][hapmap]
rs3128371	0.93[ASN][1000 genomes]
rs3128372	1.00[ASN][1000 genomes]
rs3128373	0.90[ASN][1000 genomes]
rs4433390	0.90[ASN][1000 genomes]
rs5021965	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv2454	chr1:112813849-112858259	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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

Variant related diseases (count:1)

Disease	PMID	Source
Cognitive performance	20125193	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7555668	ARL9	trans	cerebellum	SCAN
rs7555668	CEPT1	cis	cerebellum	SCAN

Chromatin state (count:14 , 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	chr1:112854800-112856600	Enhancers	Ovary	ovary
5	chr1:112854800-112856800	Bivalent Enhancer	Fetal Stomach	stomach
6	chr1:112854800-112857400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr1:112855600-112856800	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr1:112855600-112858800	Weak transcription	Fetal Lung	lung
9	chr1:112855600-112859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:112855600-112859200	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:112855800-112859800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:112856400-112856600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:112856400-112859200	Weak transcription	HSMMtube	muscle
14	chr1:112856400-112863200	Enhancers	Adipose Nuclei	Adipose

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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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