Variant report

Variant	rs56071531
Chromosome Location	chr1:179498132-179498133
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179497716..179500017-chr1:179555604..179558025,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227141	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10494517	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10494518	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11577538	0.88[ASN][1000 genomes]
rs11581440	0.84[ASN][1000 genomes]
rs11584680	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11585517	0.90[EUR][1000 genomes]
rs11586725	0.88[ASN][1000 genomes]
rs11808258	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566954	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1410585	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16854244	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1854337	0.86[ASN][1000 genomes]
rs2149399	0.82[ASN][1000 genomes]
rs2209922	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274626	0.85[ASN][1000 genomes]
rs2296960	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754132	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4111171	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41267596	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4651041	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4651042	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652400	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4652405	0.84[ASN][1000 genomes]
rs4652406	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652407	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652408	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652411	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4652412	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55908143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56237305	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57340322	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425571	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425572	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425574	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657452	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6658180	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72704417	0.89[EUR][1000 genomes]
rs72704467	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs72704477	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7512638	0.84[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7519700	0.88[ASN][1000 genomes]
rs7529107	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541890	0.88[ASN][1000 genomes]
rs7541899	0.88[ASN][1000 genomes]
rs7548654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551440	0.84[ASN][1000 genomes]
rs7551610	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9286930	0.85[ASN][1000 genomes]
rs962428	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs964983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs56071531	TDRD5	cis	Thyroid	GTEx
rs56071531	TDRD5	cis	Artery Aorta	GTEx
rs56071531	TDRD5	cis	Esophagus Mucosa	GTEx
rs56071531	TDRD5	cis	Artery Tibial	GTEx
rs56071531	TDRD5	cis	Skin Sun Exposed Lower leg	GTEx
rs56071531	RP11-545A16.3	cis	Artery Aorta	GTEx
rs56071531	TDRD5	cis	Nerve Tibial	GTEx
rs56071531	TDRD5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179486400-179499600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179486600-179499600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:179487200-179515000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:179494200-179498400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:179496200-179498200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr1:179497000-179499600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:179497200-179498200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr1:179497200-179498200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr1:179497200-179498400	Enhancers	H9 Cell Line	embryonic stem cell
10	chr1:179497200-179498800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:179497200-179499200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:179497200-179499200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:179497400-179498600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:179497400-179498600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:179498000-179499200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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