Variant report

Variant	rs12564117
Chromosome Location	chr1:179625501-179625502
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	chr1:179601826..179604447-chr1:179622966..179625873,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10157829	0.89[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10494522	0.80[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10798709	0.89[CEU][hapmap]
rs10913846	0.82[CEU][hapmap]
rs10913863	0.89[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs11578278	0.81[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs11806102	0.93[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs12021675	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12035247	0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12039153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12042409	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12045588	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2274622	0.83[GIH][hapmap]
rs4072098	0.93[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.80[LWK][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap]
rs4233182	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap]
rs4408116	0.89[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs4474210	0.88[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4483370	0.80[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4520380	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4651045	0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs4652429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4652432	0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs4652433	0.89[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs4652434	0.89[CEU][hapmap]
rs4652438	0.80[GIH][hapmap];0.88[MEX][hapmap]
rs4652442	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58593782	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6425580	0.89[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs6425581	0.85[CEU][hapmap]
rs6425588	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6672701	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs6689426	0.87[GIH][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6691856	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6692069	0.89[CEU][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6699527	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs74132225	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7513095	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7519436	0.93[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap]
rs7520355	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7540303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547484	0.93[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7547988	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9661439	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9661468	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9662949	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013000	chr1:179589193-179628536	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12564117	TDRD5	cis	Nerve Tibial	GTEx
rs12564117	TDRD5	cis	parietal	SCAN
rs12564117	TDRD5	cis	Esophagus Mucosa	GTEx
rs12564117	LHX4	cis	cerebellum	SCAN
rs12564117	TDRD5	cis	Adipose Subcutaneous	GTEx
rs12564117	TDRD5	cis	Artery Aorta	GTEx
rs12564117	AXDND1	cis	Thyroid	GTEx
rs12564117	TDRD5	cis	Thyroid	GTEx
rs12564117	NPHS2	cis	cerebellum	SCAN
rs12564117	TDRD5	cis	cerebellum	SCAN

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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