Variant report

Variant	rs6040190
Chromosome Location	chr20:10819060-10819061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16991987	1.00[AMR][1000 genomes]
rs56348465	1.00[AMR][1000 genomes]
rs58036995	1.00[AMR][1000 genomes]
rs58565167	1.00[AMR][1000 genomes]
rs6032968	1.00[AMR][1000 genomes]
rs6040193	1.00[AMR][1000 genomes]
rs7261930	1.00[AMR][1000 genomes]
rs7265005	1.00[AMR][1000 genomes]
rs7274741	1.00[AMR][1000 genomes]
rs73896403	1.00[AMR][1000 genomes]
rs73898834	1.00[AMR][1000 genomes]
rs73898836	1.00[AMR][1000 genomes]
rs73898841	1.00[AMR][1000 genomes]
rs73898852	1.00[AMR][1000 genomes]
rs73898854	1.00[AMR][1000 genomes]
rs73898858	1.00[AMR][1000 genomes]
rs73898860	1.00[AMR][1000 genomes]
rs73898863	1.00[AMR][1000 genomes]
rs73898864	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73898866	1.00[AMR][1000 genomes]
rs73898870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522874	chr20:9899439-10819210	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6040190	JARID2	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:10813200-10822400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:10818400-10819200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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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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