Variant report

Variant	rs12409744
Chromosome Location	chr1:186657271-186657272
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10798048	0.87[CEU][hapmap]
rs10911876	0.87[CEU][hapmap]
rs10911878	0.87[CEU][hapmap]
rs10911886	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs10911900	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911901	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911903	0.84[ASN][1000 genomes]
rs10911904	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs10911905	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs10911907	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911908	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911909	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10911910	0.93[ASN][1000 genomes]
rs10911911	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1119066	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119230	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1119231	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11583191	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11584118	0.84[ASN][1000 genomes]
rs12057695	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs12064238	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076624	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081510	1.00[CHB][hapmap]
rs12084433	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12089049	0.84[ASN][1000 genomes]
rs12401885	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12402603	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12404145	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12405541	0.84[ASN][1000 genomes]
rs1474596	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs20417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs20432	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066826	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2143416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179555	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2383515	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2383516	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2383529	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2891247	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4422959	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648250	0.80[ASN][1000 genomes]
rs4648276	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4648306	0.84[ASN][1000 genomes]
rs4648308	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60203808	0.80[EUR][1000 genomes]
rs61532952	0.84[ASN][1000 genomes]
rs66494422	0.84[ASN][1000 genomes]
rs6665419	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6666199	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685280	1.00[ASN][1000 genomes]
rs6698048	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67804662	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67816471	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68096880	0.84[ASN][1000 genomes]
rs689465	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72721568	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7512750	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs7533973	0.80[EUR][1000 genomes]
rs7539054	0.81[AFR][1000 genomes]
rs964571	0.84[ASN][1000 genomes]
rs9783017	0.84[ASN][1000 genomes]
rs9783052	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv470750	chr1:186642429-186700959	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv548403	chr1:186642429-186700959	Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466261	chr1:186652395-186742947	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv548405	chr1:186652395-186742947	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186657200-186657400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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