Variant report

Variant	rs13200214
Chromosome Location	chr6:28017250-28017251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27859381..27860988-chr6:28015377..28018182,2	K562	blood:

Variant related genes	Relation type
ENSG00000197153	Chromatin interaction
ENSG00000233224	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs13193295	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13194781	0.82[EUR][1000 genomes]
rs13195291	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13197574	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13197633	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13199649	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13199772	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13199906	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13201308	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13203816	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13204012	1.00[CEU][hapmap]
rs13205211	1.00[CEU][hapmap]
rs13205911	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13212651	0.82[EUR][1000 genomes]
rs13216117	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13217984	0.84[EUR][1000 genomes]
rs13218875	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs149943	0.83[CEU][hapmap]
rs149949	0.83[EUR][1000 genomes]
rs149990	0.83[CEU][hapmap]
rs17695758	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17763089	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs200948	0.91[CEU][hapmap]
rs200949	0.91[CEU][hapmap]
rs200953	0.91[CEU][hapmap]
rs200954	0.91[CEU][hapmap]
rs200977	0.91[CEU][hapmap]
rs200981	0.89[CEU][hapmap]
rs202906	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs28360499	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34166054	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34194357	0.82[EUR][1000 genomes]
rs34243448	1.00[AFR][1000 genomes]
rs34371502	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34505829	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34588114	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34765154	0.84[EUR][1000 genomes]
rs34788973	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34832585	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35001169	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35098436	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35345226	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35656932	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35749575	0.84[EUR][1000 genomes]
rs35781323	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35819751	0.82[EUR][1000 genomes]
rs35902873	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs36101351	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36116761	0.82[EUR][1000 genomes]
rs45509595	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61742093	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66868086	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66886492	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs67040724	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67297533	0.81[EUR][1000 genomes]
rs68188794	1.00[AFR][1000 genomes]
rs71537572	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71559054	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71559070	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs71559072	0.84[EUR][1000 genomes]
rs72846780	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs72846794	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv883513	chr6:27982152-28033087	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv981052	chr6:27987196-28024382	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13200214	AL022393.7	cis	Muscle Skeletal	GTEx
rs13200214	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13200214	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs13200214	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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