Variant report

Variant	rs4664090
Chromosome Location	chr2:153045144-153045145
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	chr2:153030777..153036056-chr2:153040365..153046527,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10182046	0.89[EUR][1000 genomes]
rs10194916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200231	0.89[EUR][1000 genomes]
rs10930984	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10930988	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11683326	0.90[EUR][1000 genomes]
rs11684002	0.94[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684622	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11695538	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12999722	0.87[EUR][1000 genomes]
rs13023172	0.93[EUR][1000 genomes]
rs13025274	0.86[EUR][1000 genomes]
rs13027360	0.89[EUR][1000 genomes]
rs16831021	0.82[JPT][hapmap]
rs17326195	0.91[TSI][hapmap]
rs17398246	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs17398253	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs17398399	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1987371	0.90[EUR][1000 genomes]
rs2004544	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2345644	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2345646	0.93[EUR][1000 genomes]
rs2345811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2345816	0.93[EUR][1000 genomes]
rs2345886	0.93[EUR][1000 genomes]
rs2345887	0.93[EUR][1000 genomes]
rs2345888	0.92[EUR][1000 genomes]
rs2345889	0.93[EUR][1000 genomes]
rs2345890	0.93[EUR][1000 genomes]
rs2345891	0.93[EUR][1000 genomes]
rs2345892	0.93[EUR][1000 genomes]
rs2345893	0.87[EUR][1000 genomes]
rs2345894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2345897	0.93[EUR][1000 genomes]
rs2345900	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2881237	0.92[EUR][1000 genomes]
rs2881238	0.93[EUR][1000 genomes]
rs2881242	0.89[EUR][1000 genomes]
rs35451141	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4233656	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233657	0.93[EUR][1000 genomes]
rs4254462	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4284784	0.86[EUR][1000 genomes]
rs4293527	0.93[EUR][1000 genomes]
rs4316898	0.93[EUR][1000 genomes]
rs4664092	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4664548	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4664549	0.93[EUR][1000 genomes]
rs4664551	0.93[EUR][1000 genomes]
rs4664552	0.93[EUR][1000 genomes]
rs4664556	0.87[EUR][1000 genomes]
rs4664558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs56853020	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60098187	0.86[EUR][1000 genomes]
rs60847003	0.86[EUR][1000 genomes]
rs6433898	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6433929	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6433933	0.92[EUR][1000 genomes]
rs6433935	0.93[EUR][1000 genomes]
rs6433940	0.92[EUR][1000 genomes]
rs66529470	0.93[EUR][1000 genomes]
rs66673544	0.82[EUR][1000 genomes]
rs66733611	0.86[EUR][1000 genomes]
rs6712158	0.93[EUR][1000 genomes]
rs67135983	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67157738	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6726065	0.92[EUR][1000 genomes]
rs6729673	0.93[EUR][1000 genomes]
rs6745311	0.82[EUR][1000 genomes]
rs6747394	0.92[EUR][1000 genomes]
rs6750417	0.92[EUR][1000 genomes]
rs6750670	0.92[EUR][1000 genomes]
rs67874818	0.93[EUR][1000 genomes]
rs68008008	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68036808	0.93[EUR][1000 genomes]
rs72857737	0.93[EUR][1000 genomes]
rs72864740	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72864741	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72864754	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72864765	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73002815	0.93[EUR][1000 genomes]
rs7570050	0.93[EUR][1000 genomes]
rs7579128	0.93[EUR][1000 genomes]
rs7580423	0.85[AFR][1000 genomes]
rs7584558	0.86[EUR][1000 genomes]
rs7586518	0.92[EUR][1000 genomes]
rs7596540	0.86[EUR][1000 genomes]
rs7597103	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7600346	0.90[EUR][1000 genomes]
rs9750400	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4664090	CACNB4	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
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