Variant report

Variant	rs543338
Chromosome Location	chr10:89971647-89971648
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1147648	0.93[EUR][1000 genomes]
rs1943987	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs485396	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508901	0.93[EUR][1000 genomes]
rs533722	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs535541	0.93[EUR][1000 genomes]
rs537546	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs545874	0.91[ASN][1000 genomes]
rs551265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567645	0.93[EUR][1000 genomes]
rs629959	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs645516	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647730	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv895878	chr10:89959082-90006507	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs543338	CD7	trans	cerebellum	SCAN
rs543338	ANKRD1	cis	cerebellum	SCAN
rs543338	LRIT2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89955400-89998000	Weak transcription	Aorta	Aorta
2	chr10:89966400-89973000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr10:89967800-89978200	Weak transcription	Pancreas	Pancrea
4	chr10:89968000-89972400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr10:89968800-89974800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:89969000-89972600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr10:89969200-89979400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr10:89969600-89974000	Weak transcription	GM12878-XiMat	blood
9	chr10:89969600-89974400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:89970600-89978000	Weak transcription	Right Atrium	heart
11	chr10:89970800-89980600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:89971200-89978200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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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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