Variant report

Variant	rs12899020
Chromosome Location	chr15:83468813-83468814
allele	A/G
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:9)

rs_ID	r²[population]
rs12900374	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs12915294	0.87[EUR][1000 genomes]
rs12915384	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs1877240	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs35270670	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35946485	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs36111056	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4617830	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7178859	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv977072	chr15:83467994-83473044	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12899020	AP3B2	cis	lung	GTEx
rs12899020	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs12899020	AP3B2	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83450400-83477600	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:83467400-83470400	Enhancers	Fetal Heart	heart
3	chr15:83467800-83469000	Enhancers	Psoas Muscle	Psoas
4	chr15:83467800-83469200	Enhancers	Fetal Muscle Leg	muscle
5	chr15:83468200-83469000	Enhancers	Fetal Muscle Trunk	muscle
6	chr15:83468200-83469000	Enhancers	Left Ventricle	heart
7	chr15:83468200-83469000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr15:83468400-83469200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
9	chr15:83468600-83469200	Enhancers	Right Atrium	heart
10	chr15:83468800-83469800	Weak transcription	K562	blood
11	chr15:83468800-83470200	Weak transcription	Right Ventricle	heart

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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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