Variant report

Variant	rs3005799
Chromosome Location	chr1:112815153-112815154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2998335	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121989	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3128364	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3128365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3128366	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs3128367	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4294408	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676747	0.92[ASN][1000 genomes]
rs9429470	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[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	esv3425142	chr1:112811829-112815427	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
3	nsv2454	chr1:112813849-112858259	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3005799	CEPT1	cis	cerebellum	SCAN
rs3005799	MOV10	cis	parietal	SCAN
rs3005799	CSDE1	cis	cerebellum	SCAN
rs3005799	AHCYL1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112808200-112815200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:112811400-112815200	Weak transcription	Right Atrium	heart
3	chr1:112813600-112815200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:112814200-112815800	Enhancers	GM12878-XiMat	blood

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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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