Variant report

Variant	rs357199
Chromosome Location	chr1:71969017-71969018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11209788	0.82[CHD][hapmap]
rs12727814	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1517759	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1607275	0.91[ASN][1000 genomes]
rs1889298	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs357200	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs357201	0.80[ASN][1000 genomes]
rs357202	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs357203	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs357206	0.91[ASN][1000 genomes]
rs357208	0.80[ASN][1000 genomes]
rs357209	0.80[ASN][1000 genomes]
rs357210	0.95[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs357214	0.95[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs357222	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs357223	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs357225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs357228	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs357230	0.88[CHD][hapmap];0.80[AMR][1000 genomes]
rs357234	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs357237	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs6680901	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs672999	0.91[ASN][1000 genomes]
rs7553624	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949599	chr1:71655652-72327802	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv916508	chr1:71777392-72046388	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv546474	chr1:71793221-72040354	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv830170	chr1:71856447-72008758	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs357199	LHX8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71968200-71969200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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