Variant report

Variant	rs6689426
Chromosome Location	chr1:179569722-179569723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179559457..179562076-chr1:179568845..179571260,2	MCF-7	breast:
2	chr1:179569100..179571414-chr20:16483779..16486109,2	MCF-7	breast:
3	chr1:179558595..179562573-chr1:179564810..179570275,6	MCF-7	breast:
4	chr1:179567719..179570600-chr1:179574245..179576167,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261060	Chromatin interaction
ENSG00000162782	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10157829	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10494517	0.86[JPT][hapmap]
rs10494518	0.86[JPT][hapmap]
rs10494522	0.83[GIH][hapmap]
rs1079291	0.82[ASN][1000 genomes]
rs10798709	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10913846	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs10913863	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs11578278	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs11585517	0.86[JPT][hapmap]
rs11589161	0.89[JPT][hapmap]
rs11806102	0.83[GIH][hapmap]
rs11808258	0.86[JPT][hapmap]
rs12021675	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12035247	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042409	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12045588	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12564117	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs1410593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1999068	0.94[ASN][1000 genomes]
rs2209922	0.86[JPT][hapmap]
rs2274622	0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3765547	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4072098	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs4111171	0.81[JPT][hapmap]
rs4233182	0.83[GIH][hapmap]
rs4408116	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs4474210	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4483370	0.83[GIH][hapmap]
rs4520380	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4651045	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs4652406	0.85[JPT][hapmap]
rs4652412	0.86[JPT][hapmap]
rs4652432	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs4652433	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs4652434	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4652438	0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs55635521	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58593782	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61310274	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425574	0.85[JPT][hapmap]
rs6425580	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs6425581	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6425585	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6425588	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6668120	0.81[JPT][hapmap]
rs6672701	0.89[GIH][hapmap];0.81[TSI][hapmap]
rs6674086	0.81[JPT][hapmap]
rs6691856	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6692069	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6699527	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs74132225	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs744446	0.94[ASN][1000 genomes]
rs7519436	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs7520355	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7540303	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7547484	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7547988	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs964983	0.86[JPT][hapmap]
rs964984	0.86[JPT][hapmap]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6689426	TDRD5	cis	cerebellum	SCAN
rs6689426	TDRD5	cis	parietal	SCAN
rs6689426	TDRD5	cis	Adipose Subcutaneous	GTEx
rs6689426	TDRD5	cis	Esophagus Mucosa	GTEx
rs6689426	TDRD5	cis	Nerve Tibial	GTEx
rs6689426	TDRD5	cis	Thyroid	GTEx
rs6689426	TDRD5	cis	Artery Aorta	GTEx
rs6689426	TDRD5	cis	Artery Tibial	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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