Variant report

Variant	rs6674086
Chromosome Location	chr1:179459554-179459555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10494517	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs10494518	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs11577538	0.87[ASW][hapmap];0.87[MKK][hapmap]
rs11581470	0.87[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs11584680	0.95[EUR][1000 genomes]
rs11585517	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11586725	0.87[YRI][hapmap]
rs11808258	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs12021675	0.80[JPT][hapmap]
rs12566954	0.92[EUR][1000 genomes]
rs13306732	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1410585	0.92[EUR][1000 genomes]
rs1410593	0.81[JPT][hapmap]
rs16854042	0.86[CEU][hapmap];0.90[JPT][hapmap]
rs16854244	0.92[EUR][1000 genomes]
rs2209922	1.00[ASW][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2274622	0.87[ASW][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs2296960	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes]
rs3765547	0.92[CHD][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap]
rs4072451	0.87[CEU][hapmap];0.84[JPT][hapmap]
rs4072452	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs4111171	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41267596	0.90[EUR][1000 genomes]
rs4651029	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4651041	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4651042	0.94[EUR][1000 genomes]
rs4652367	0.83[CHB][hapmap]
rs4652369	0.86[JPT][hapmap]
rs4652380	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs4652400	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4652406	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs4652407	0.94[EUR][1000 genomes]
rs4652408	0.94[EUR][1000 genomes]
rs4652411	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4652412	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs55908143	0.94[EUR][1000 genomes]
rs56071531	0.94[EUR][1000 genomes]
rs56237305	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57340322	0.88[EUR][1000 genomes]
rs59559400	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425557	0.87[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs6425571	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425572	0.92[EUR][1000 genomes]
rs6425574	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs6656056	0.83[EUR][1000 genomes]
rs6657452	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6658180	0.91[EUR][1000 genomes]
rs6666455	0.87[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs6668120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6679542	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs6689426	0.81[JPT][hapmap]
rs6693527	0.83[EUR][1000 genomes]
rs6698526	0.82[EUR][1000 genomes]
rs6700149	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs72704417	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72704467	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72704477	0.85[EUR][1000 genomes]
rs72719243	0.83[EUR][1000 genomes]
rs7413415	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7512638	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7521291	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7529107	0.84[EUR][1000 genomes]
rs7541890	0.87[YRI][hapmap]
rs7543334	0.92[ASN][1000 genomes]
rs7548654	0.93[EUR][1000 genomes]
rs7551610	1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs962428	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs964983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs964984	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs9660976	0.83[EUR][1000 genomes]
rs9726734	0.82[EUR][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	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	esv3505459	chr1:179454879-179459677	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	esv1826150	chr1:179455645-179469253	Inactive region	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	esv1820823	chr1:179455645-179479803	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv548328	chr1:179456359-179459554	Inactive region	TF binding region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6674086	TDRD5	cis	Thyroid	GTEx
rs6674086	TDRD5	cis	Skin Sun Exposed Lower leg	GTEx
rs6674086	TDRD5	cis	parietal	SCAN
rs6674086	TDRD5	cis	Nerve Tibial	GTEx
rs6674086	TDRD5	cis	cerebellum	SCAN
rs6674086	TDRD5	cis	Artery Aorta	GTEx
rs6674086	SOAT1	cis	cerebellum	SCAN
rs6674086	GPR52	cis	cerebellum	SCAN
rs6674086	TDRD5	cis	Artery Tibial	GTEx
rs6674086	RASAL2	cis	parietal	SCAN
rs6674086	TDRD5	cis	Esophagus Mucosa	GTEx
rs6674086	RP11-545A16.3	cis	Artery Aorta	GTEx
rs6674086	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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