Variant report

Variant	rs10494522
Chromosome Location	chr1:179606157-179606158
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	chr1:179601476..179603491-chr1:179604853..179608456,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10157829	0.83[GIH][hapmap];0.83[MEX][hapmap]
rs10913863	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs11806102	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs12021675	0.80[AMR][1000 genomes]
rs12035247	0.83[GIH][hapmap];0.87[MEX][hapmap]
rs12039153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12564117	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]
rs4072098	0.83[GIH][hapmap]
rs4233182	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs4408116	0.85[GIH][hapmap];0.87[MEX][hapmap]
rs4474210	0.87[ASW][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs4483370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651045	0.83[GIH][hapmap];0.87[MEX][hapmap]
rs4652429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4652432	0.83[GIH][hapmap];0.87[MEX][hapmap]
rs4652433	0.83[GIH][hapmap]
rs4652438	0.89[CEU][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap]
rs6425580	0.83[GIH][hapmap]
rs6425585	0.89[CEU][hapmap]
rs6659507	0.82[EUR][1000 genomes]
rs6672701	0.87[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap]
rs6689426	0.83[GIH][hapmap]
rs7513095	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7519436	0.83[GIH][hapmap];0.87[MEX][hapmap]
rs7540303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7547484	0.83[GIH][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]

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	nsv1013000	chr1:179589193-179628536	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
2	esv3394963	chr1:179605329-179609927	Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	nsv511147	chr1:179606157-179608461	Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10494522	TDRD5	cis	parietal	SCAN
rs10494522	LHX4	cis	cerebellum	SCAN
rs10494522	TDRD5	cis	cerebellum	SCAN
rs10494522	TDRD5	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179604200-179607200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:179605400-179607200	Enhancers	Fetal Heart	heart

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