Variant report

Variant	rs11024502
Chromosome Location	chr11:18178448-18178449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18173467..18175393-chr11:18177019..18179182,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254857	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10766458	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10832890	0.84[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832893	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024503	0.82[ASN][1000 genomes]
rs11024530	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11024531	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024539	0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap];0.91[ASN][1000 genomes]
rs11603777	0.84[ASN][1000 genomes]
rs12285875	0.85[ASN][1000 genomes]
rs1378607	0.82[CHB][hapmap]
rs1378608	0.82[CHB][hapmap]
rs1378611	0.81[CHB][hapmap]
rs1378612	0.82[CHB][hapmap]
rs1531104	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs1531105	0.91[CHB][hapmap]
rs1902266	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1968730	0.91[CHB][hapmap];0.80[CHD][hapmap]
rs1968732	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2014694	0.91[CHB][hapmap]
rs2078066	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2124375	0.91[CHB][hapmap]
rs2124376	0.91[CHB][hapmap]
rs2124377	0.91[CHB][hapmap]
rs2246304	0.91[CHB][hapmap]
rs2246305	0.91[CHB][hapmap]
rs2246388	0.91[CHB][hapmap]
rs2253938	0.82[CHB][hapmap]
rs2403247	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2403248	0.91[CHB][hapmap]
rs2445165	0.82[CHB][hapmap]
rs2445180	0.86[CHB][hapmap]
rs2445182	0.91[CHB][hapmap]
rs2445183	0.91[CHB][hapmap]
rs2445203	0.81[ASN][1000 genomes]
rs2445204	0.80[ASN][1000 genomes]
rs2445205	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs2445206	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs2445207	0.82[ASN][1000 genomes]
rs2468772	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs2468774	0.86[CHB][hapmap]
rs2468820	0.82[ASN][1000 genomes]
rs2468824	0.82[CHB][hapmap]
rs2468825	0.81[CHB][hapmap]
rs2860276	0.91[CHB][hapmap]
rs2860278	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs34114573	0.82[ASN][1000 genomes]
rs4417246	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs73434204	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	esv11709	chr11:18138662-18200717	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3509521	chr11:18159957-18188401	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3509522	chr11:18159957-18188401	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3367251	chr11:18159957-18196082	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv518373	chr11:18164687-18195348	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv975090	chr11:18164912-18189697	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv16635	chr11:18165268-18194893	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2762898	chr11:18166780-18198880	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1038257	chr11:18169410-18198309	Enhancers Bivalent Enhancer Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11024502	SLC6A5	cis	cerebellum	SCAN
rs11024502	LDHAL6A	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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