Variant report

Variant	rs999234
Chromosome Location	chr6:166711287-166711288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10946152	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10946158	0.80[AMR][1000 genomes]
rs12198613	0.82[AMR][1000 genomes]
rs12214281	0.81[AMR][1000 genomes]
rs12214812	0.82[AMR][1000 genomes]
rs12662924	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4144886	0.82[AMR][1000 genomes]
rs55936781	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59337176	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6932631	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6938819	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73263155	0.80[EUR][1000 genomes]
rs7740965	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7748966	0.82[EUR][1000 genomes]
rs9348115	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348116	0.91[AMR][1000 genomes];0.99[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	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv886935	chr6:166704744-166726566	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs999234	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL
rs999234	SFT2D1	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166708200-166712000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:166710600-166712000	Weak transcription	Brain Angular Gyrus	brain
3	chr6:166710800-166711600	Active TSS	Brain Cingulate Gyrus	brain
4	chr6:166710800-166712000	Weak transcription	Brain Anterior Caudate	brain
5	chr6:166711000-166712000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:166711000-166712000	Weak transcription	Brain Substantia Nigra	brain
7	chr6:166711000-166714400	Enhancers	Brain Hippocampus Middle	brain
8	chr6:166711200-166711400	Bivalent Enhancer	Fetal Muscle Trunk	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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