Variant report

Variant	rs12790525
Chromosome Location	chr11:57822450-57822451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1113334	0.85[ASN][1000 genomes]
rs1113335	0.85[ASN][1000 genomes]
rs11600060	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs11601202	0.88[ASN][1000 genomes]
rs11601223	0.87[ASN][1000 genomes]
rs11601663	0.88[ASN][1000 genomes]
rs11601841	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs11604473	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs11604630	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs11605988	0.92[ASN][1000 genomes]
rs11606464	0.92[ASN][1000 genomes]
rs11607308	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608016	0.88[ASN][1000 genomes]
rs12792435	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12792638	0.87[ASN][1000 genomes]
rs12801976	0.85[ASN][1000 genomes]
rs12805812	0.92[CEU][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1376489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17152376	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs1814059	0.92[CEU][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2089747	0.85[ASN][1000 genomes]
rs2441952	0.84[CEU][hapmap]
rs34015013	0.88[ASN][1000 genomes]
rs34300518	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35163247	0.88[ASN][1000 genomes]
rs35742790	0.88[ASN][1000 genomes]
rs36071925	0.92[ASN][1000 genomes]
rs3862656	0.87[AMR][1000 genomes]
rs4509781	0.96[CEU][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61902775	0.89[AMR][1000 genomes]
rs61902797	0.87[AMR][1000 genomes]
rs61902798	0.84[AMR][1000 genomes]
rs61902799	0.85[AMR][1000 genomes]
rs61903966	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs61903967	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs61904009	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61904011	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61904024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905309	0.88[ASN][1000 genomes]
rs67305834	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7113760	0.92[CEU][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7120102	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs7120442	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs7121128	0.85[ASN][1000 genomes]
rs7123727	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7929515	0.88[ASN][1000 genomes]
rs7930102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934149	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7934184	0.92[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes]
rs7935428	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs7938062	0.92[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes]
rs7945154	0.90[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes]
rs7949558	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs930703	0.92[CEU][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832165	chr11:57806024-58009076	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57813600-57825000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:57821600-57826000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr11:57821800-57825000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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