Variant report

Variant	rs4111171
Chromosome Location	chr1:179476746-179476747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179464371..179466688-chr1:179474524..179476785,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10494517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10494518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913765	0.83[CHB][hapmap]
rs11577538	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11581440	0.82[ASN][1000 genomes]
rs11581470	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11584680	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11585517	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs11586725	0.87[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs11808258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12566954	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12743373	0.82[CHB][hapmap]
rs12749731	0.81[CHB][hapmap]
rs12757065	0.82[CHB][hapmap]
rs13306732	0.83[CEU][hapmap]
rs1410585	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1410593	0.82[JPT][hapmap]
rs16854042	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs16854244	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1854337	0.81[ASN][1000 genomes]
rs2149399	0.91[CHB][hapmap]
rs2209922	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274622	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs2274626	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2296960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3754132	0.81[ASN][1000 genomes]
rs3765547	0.86[JPT][hapmap];0.85[YRI][hapmap]
rs4072451	0.88[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4072452	0.88[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap]
rs41267596	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4400577	0.83[CHB][hapmap]
rs4424468	0.83[CHB][hapmap]
rs4651025	0.82[CHB][hapmap]
rs4651029	0.82[EUR][1000 genomes]
rs4651041	0.96[EUR][1000 genomes]
rs4651042	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4652369	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs4652374	0.82[CHB][hapmap]
rs4652380	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs4652400	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4652406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4652407	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4652408	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4652411	0.95[EUR][1000 genomes]
rs4652412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55908143	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56071531	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56237305	0.95[EUR][1000 genomes]
rs57340322	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59559400	0.81[EUR][1000 genomes]
rs6425557	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6425571	0.95[EUR][1000 genomes]
rs6425572	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656056	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6657452	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6658180	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6664339	0.86[CHB][hapmap]
rs6666455	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs6668120	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6674086	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6678667	0.82[CHB][hapmap]
rs6679542	0.96[JPT][hapmap]
rs6689426	0.81[JPT][hapmap]
rs6690348	0.83[CHB][hapmap]
rs6693527	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6693627	0.83[CHB][hapmap]
rs6698526	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6700149	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs72704417	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72704467	0.95[EUR][1000 genomes]
rs72704477	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72719243	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7413415	0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap]
rs7512638	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs7519700	0.83[ASN][1000 genomes]
rs7521291	0.82[EUR][1000 genomes]
rs7529107	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7541890	0.87[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs7541899	0.83[ASN][1000 genomes]
rs7548654	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7551440	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs7551610	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9286930	0.80[ASN][1000 genomes]
rs962428	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs964983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs964984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9660976	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9726734	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4111171	TDRD5	cis	Skin Sun Exposed Lower leg	GTEx
rs4111171	TDRD5	cis	Nerve Tibial	GTEx
rs4111171	RP11-545A16.3	cis	Artery Aorta	GTEx
rs4111171	TDRD5	cis	Artery Aorta	GTEx
rs4111171	TDRD5	cis	Thyroid	GTEx
rs4111171	TDRD5	cis	Artery Tibial	GTEx
rs4111171	TDRD5	cis	Adipose Subcutaneous	GTEx
rs4111171	TDRD5	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179476400-179476800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:179476600-179477800	Enhancers	Stomach Mucosa	stomach

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