Variant report

Variant	rs12739607
Chromosome Location	chr1:179387841-179387842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10913755	0.91[AMR][1000 genomes]
rs10913760	0.90[AMR][1000 genomes]
rs10913761	0.90[AMR][1000 genomes]
rs10913762	0.87[AMR][1000 genomes]
rs10913766	0.90[AMR][1000 genomes]
rs10913767	0.91[AMR][1000 genomes]
rs10913768	0.88[AMR][1000 genomes]
rs10913769	0.88[AMR][1000 genomes]
rs10913770	0.91[AMR][1000 genomes]
rs10913771	0.88[AMR][1000 genomes]
rs11577579	0.91[AMR][1000 genomes]
rs11578241	0.91[AMR][1000 genomes]
rs11582255	0.91[AMR][1000 genomes]
rs11582293	0.91[AMR][1000 genomes]
rs11582754	0.88[AMR][1000 genomes]
rs11586744	0.94[AMR][1000 genomes]
rs11802624	0.90[AMR][1000 genomes]
rs11802625	0.90[AMR][1000 genomes]
rs11802637	0.90[AMR][1000 genomes]
rs11807559	0.83[AMR][1000 genomes]
rs12401957	0.91[AMR][1000 genomes]
rs12408443	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12409337	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12722736	0.91[AMR][1000 genomes]
rs12724496	0.91[AMR][1000 genomes]
rs12724634	0.91[AMR][1000 genomes]
rs12725414	0.83[AMR][1000 genomes]
rs12726875	0.83[AMR][1000 genomes]
rs12729775	0.91[AMR][1000 genomes]
rs12738929	0.91[AMR][1000 genomes]
rs12739116	0.91[AMR][1000 genomes]
rs12744251	0.91[AMR][1000 genomes]
rs12744438	0.83[AMR][1000 genomes]
rs12744949	0.83[AMR][1000 genomes]
rs12746253	0.83[AMR][1000 genomes]
rs12746578	0.83[AMR][1000 genomes]
rs12750591	0.91[AMR][1000 genomes]
rs12751260	0.83[AMR][1000 genomes]
rs12757935	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12758415	0.94[AMR][1000 genomes]
rs12760048	0.83[AMR][1000 genomes]
rs12760534	0.81[AMR][1000 genomes]
rs4130266	0.88[AMR][1000 genomes]
rs4233177	0.83[AMR][1000 genomes]
rs4233178	0.83[AMR][1000 genomes]
rs4418554	0.88[AMR][1000 genomes]
rs4454499	0.91[AMR][1000 genomes]
rs4651028	0.91[AMR][1000 genomes]
rs61821011	0.88[AMR][1000 genomes]
rs7513782	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7513973	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7532155	0.88[AMR][1000 genomes]
rs7551894	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7554103	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9662026	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
2	esv3514400	chr1:179349344-179400533	Enhancers Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3514401	chr1:179349344-179400533	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3451112	chr1:179352344-179400533	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1819329	chr1:179371973-179442337	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv548298	chr1:179376896-179436288	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12739607	TDRD5	cis	Artery Tibial	GTEx
rs12739607	TDRD5	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179387000-179389000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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