Variant report

Variant	rs4652400
Chromosome Location	chr1:179450591-179450592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179450571..179452564-chr1:179459735..179462060,2	K562	blood:
2	chr1:179445378..179447823-chr1:179449930..179453030,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10494517	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10494518	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11584680	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11808258	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12566954	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1410585	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16854244	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2209922	0.87[ASN][1000 genomes]
rs2296960	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4111171	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41267596	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4651029	0.87[EUR][1000 genomes]
rs4651041	0.89[EUR][1000 genomes]
rs4651042	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4652406	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4652407	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4652408	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4652411	0.88[EUR][1000 genomes]
rs4652412	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55908143	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56071531	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56237305	0.88[EUR][1000 genomes]
rs57340322	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59559400	0.87[EUR][1000 genomes]
rs6425557	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6425571	0.88[EUR][1000 genomes]
rs6425572	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425574	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6656056	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6657452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6658180	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6693527	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6698526	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72704417	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs72704467	0.88[EUR][1000 genomes]
rs72704477	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72719243	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7512638	0.88[EUR][1000 genomes]
rs7521291	0.88[EUR][1000 genomes]
rs7529107	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7548654	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7551610	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs962428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs964983	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs964984	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9660976	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9726734	0.86[EUR][1000 genomes];0.81[ASN][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	nsv466217	chr1:179371973-179477921	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv548297	chr1:179371973-179477921	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1009624	chr1:179423063-179459676	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	nsv1011557	chr1:179426390-179459460	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4652400	TDRD5	cis	Esophagus Mucosa	GTEx
rs4652400	TDRD5	cis	Nerve Tibial	GTEx
rs4652400	TDRD5	cis	Artery Aorta	GTEx
rs4652400	TDRD5	cis	Artery Tibial	GTEx
rs4652400	TDRD5	cis	Thyroid	GTEx
rs4652400	RP11-545A16.3	cis	Artery Aorta	GTEx
rs4652400	TDRD5	cis	Skin Sun Exposed Lower leg	GTEx
rs4652400	TDRD5	cis	Adipose Subcutaneous	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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