Variant report

Variant	rs7529107
Chromosome Location	chr1:179512630-179512631
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179510342..179513205-chr1:179522865..179525249,2	MCF-7	breast:
2	chr1:179510162..179513711-chr1:179513904..179516885,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPHS2-1	chr1:179512336-179515388	ENSG00000261250.1

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10494517	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10494518	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11577538	0.88[ASN][1000 genomes]
rs11584680	0.80[EUR][1000 genomes]
rs11585517	0.93[EUR][1000 genomes]
rs11586725	0.88[ASN][1000 genomes]
rs11808258	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12566954	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1410585	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16854244	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2209922	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2274626	0.85[ASN][1000 genomes]
rs2296960	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754132	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4111171	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41267596	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4651041	0.90[EUR][1000 genomes]
rs4651042	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4652400	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4652406	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4652407	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4652408	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4652411	0.91[EUR][1000 genomes]
rs4652412	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55908143	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56071531	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56237305	0.91[EUR][1000 genomes]
rs57340322	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425571	0.91[EUR][1000 genomes]
rs6425572	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6425574	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6657452	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6658180	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72704417	0.80[EUR][1000 genomes]
rs72704467	0.89[EUR][1000 genomes]
rs72704477	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7512638	0.89[EUR][1000 genomes]
rs7519700	0.88[ASN][1000 genomes]
rs7541890	0.88[ASN][1000 genomes]
rs7541899	0.88[ASN][1000 genomes]
rs7548654	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7551610	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9286930	0.85[ASN][1000 genomes]
rs962428	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs964983	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs964984	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522746	chr1:179501365-179518459	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7529107	TDRD5	cis	Artery Tibial	GTEx
rs7529107	TDRD5	cis	Adipose Subcutaneous	GTEx
rs7529107	TDRD5	cis	Thyroid	GTEx
rs7529107	TDRD5	cis	Esophagus Mucosa	GTEx
rs7529107	RP11-545A16.3	cis	Artery Aorta	GTEx
rs7529107	TDRD5	cis	Artery Aorta	GTEx
rs7529107	TDRD5	cis	Nerve Tibial	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179487200-179515000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:179510600-179520600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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