Variant report

Variant	rs66529373
Chromosome Location	chr6:28023008-28023009
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28022204..28024125-chr6:28233468..28235109,2	MCF-7	breast:
2	chr6:27856950..27859637-chr6:28022500..28024631,2	K562	blood:
3	chr6:28022742..28025114-chr6:28059303..28061030,2	K562	blood:

Variant related genes	Relation type
ENSG00000197153	Chromatin interaction
ENSG00000219891	Chromatin interaction
ENSG00000197062	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs149899	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs149946	0.81[EUR][1000 genomes]
rs149947	0.81[EUR][1000 genomes]
rs149961	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs149964	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs149968	0.83[EUR][1000 genomes]
rs149969	0.83[EUR][1000 genomes]
rs156744	0.81[EUR][1000 genomes]
rs172166	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs203890	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61471148	0.86[ASN][1000 genomes]
rs9348789	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357060	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9380045	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393881	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9468271	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9468274	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9468275	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9468277	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9468278	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv883513	chr6:27982152-28033087	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv981052	chr6:27987196-28024382	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv966688	chr6:28019147-28028399	Bivalent Enhancer	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	esv3322200	chr6:28022023-28023271	Inactive region	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	esv3390093	chr6:28022023-28024221	Inactive region	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3436863	chr6:28022773-28024221	Inactive region	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs66529373	AL022393.7	cis	Muscle Skeletal	GTEx
rs66529373	OR2B7P	cis	Thyroid	GTEx
rs66529373	ZNF192P1	cis	Heart Left Ventricle	GTEx
rs66529373	AL022393.7	cis	Heart Left Ventricle	GTEx
rs66529373	AL022393.7	cis	Nerve Tibial	GTEx
rs66529373	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs66529373	RP1-265C24.5	cis	Heart Left Ventricle	GTEx
rs66529373	OR2B8P	cis	Thyroid	GTEx
rs66529373	OR2B8P	cis	Skin Sun Exposed Lower leg	GTEx

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

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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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