Variant report

Variant	rs12739116
Chromosome Location	chr1:179417682-179417683
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr1:179417675-179418305	K562	blood:	n/a	n/a
2	CCNT2	chr1:179417639-179417843	K562	blood:	n/a	n/a
3	BHLHE40	chr1:179417644-179417794	K562	blood:	n/a	chr1:179417771-179417787
4	CTCF	chr1:179417603-179417829	K562	blood:	n/a	n/a
5	MYC	chr1:179417591-179418148	K562	blood:	n/a	n/a
6	HMGN3	chr1:179417615-179417840	K562	blood:	n/a	n/a
7	MAX	chr1:179417523-179417854	K562	blood:	n/a	n/a
8	MAX	chr1:179417629-179417860	K562	blood:	n/a	n/a
9	UBTF	chr1:179417616-179417838	K562	blood:	n/a	n/a
10	ARID3A	chr1:179417315-179418149	K562	blood:	n/a	n/a
11	E2F6	chr1:179417649-179417864	K562	blood:	n/a	chr1:179417754-179417763
12	MAX	chr1:179417610-179417825	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SOAT1-3	chr1:179417648-179417966	NONHSAT007860
2	lnc-SOAT1-3	chr1:179417648-179417967	NONHSAT007859

Variant related genes	Relation type
MEF2AP1	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10913755	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913760	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913761	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913762	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913766	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913768	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913769	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913770	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913771	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913809	0.86[ASN][1000 genomes]
rs11577579	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578241	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582158	0.86[ASN][1000 genomes]
rs11582255	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582754	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586744	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11802624	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802625	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802637	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807559	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12401957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408443	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12409337	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12722736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724778	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12724901	0.86[ASN][1000 genomes]
rs12725414	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12726875	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12729067	1.00[ASN][1000 genomes]
rs12729775	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12736279	0.86[ASN][1000 genomes]
rs12736545	0.86[ASN][1000 genomes]
rs12738929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739607	0.91[AMR][1000 genomes]
rs12741425	0.86[ASN][1000 genomes]
rs12743585	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12744251	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744438	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12744949	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12746253	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12746578	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12750591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751260	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12751550	0.80[ASN][1000 genomes]
rs12755634	0.80[ASN][1000 genomes]
rs12756624	0.86[ASN][1000 genomes]
rs12757935	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12758415	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12760048	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12760534	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1328597	0.86[ASN][1000 genomes]
rs1328598	0.86[ASN][1000 genomes]
rs1410589	0.86[ASN][1000 genomes]
rs1576224	0.80[ASN][1000 genomes]
rs2209919	0.86[ASN][1000 genomes]
rs34291276	0.86[ASN][1000 genomes]
rs34463289	0.86[ASN][1000 genomes]
rs35401719	0.86[ASN][1000 genomes]
rs35427395	0.86[ASN][1000 genomes]
rs36057553	0.81[ASN][1000 genomes]
rs4130266	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233177	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4233178	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4360491	0.93[ASN][1000 genomes]
rs4418554	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4454499	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651028	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651037	0.80[ASN][1000 genomes]
rs4652368	0.80[ASN][1000 genomes]
rs61821011	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826364	0.86[ASN][1000 genomes]
rs61826365	0.86[ASN][1000 genomes]
rs7513782	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7513973	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7532155	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551894	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7554103	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9662026	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9699789	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv946523	chr1:179417249-179426389	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12739116	TDRD5	cis	Nerve Tibial	GTEx
rs12739116	AXDND1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179417600-179418000	Active TSS	K562	blood

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