Variant report

Variant	rs4590669
Chromosome Location	chr1:112802600-112802601
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10745327	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857948	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102446	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102448	0.94[ASN][1000 genomes]
rs4491059	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513316	1.00[ASN][1000 genomes]
rs7527349	1.00[ASN][1000 genomes]
rs7554440	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[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	esv2762184	chr1:112801661-112805968	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4590669	CEPT1	cis	cerebellum	SCAN
rs4590669	SLC6A17	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112788800-112812200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:112798800-112805000	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:112799000-112803400	Weak transcription	HSMMtube	muscle
4	chr1:112800000-112805200	Weak transcription	HSMM	muscle
5	chr1:112800200-112805600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:112801600-112802800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:112801600-112804800	Weak transcription	Right Atrium	heart
8	chr1:112802000-112802600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:112802000-112806800	Weak transcription	Small Intestine	intestine
10	chr1:112802200-112805000	Weak transcription	Fetal Stomach	stomach
11	chr1:112802600-112804000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:112802600-112804200	Enhancers	Brain Substantia Nigra	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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