Variant report

Variant	rs1109282
Chromosome Location	chr3:140643243-140643244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140634376..140636295-chr3:140641836..140643560,2	MCF-7	breast:
2	chr3:140640464..140644389-chr3:140659845..140663007,5	MCF-7	breast:
3	chr3:140641570..140644550-chr3:140649016..140650744,2	K562	blood:
4	chr3:140642736..140646722-chr3:140659939..140663193,5	K562	blood:

Variant related genes	Relation type
ENSG00000114120	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1047330	1.00[CHB][hapmap]
rs1056126	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1056127	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10935413	0.82[ASN][1000 genomes]
rs10935414	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1109283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11707116	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11710204	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11710926	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11711131	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11713505	0.85[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11713816	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs11714438	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715248	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11717097	0.81[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11717620	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11718040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11718539	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs11718563	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11720342	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12486226	0.82[JPT][hapmap]
rs12489397	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1568337	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs1593624	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16850915	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16850917	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16850921	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16850924	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16850926	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292919	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2310859	0.88[ASN][1000 genomes]
rs2555702	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2555707	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs2871615	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35140461	0.80[ASN][1000 genomes]
rs3755764	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755765	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773835	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773837	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773838	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4380393	0.85[EUR][1000 genomes]
rs4524250	0.81[ASN][1000 genomes]
rs57151068	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57526660	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57799705	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59128309	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59221985	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61052022	0.85[EUR][1000 genomes]
rs61151473	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61629363	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61708145	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439962	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6785007	0.80[ASN][1000 genomes]
rs6810200	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72991025	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72991046	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7621150	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7624649	0.82[JPT][hapmap]
rs7626525	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7632043	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637899	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7638206	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7643287	0.94[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs7643434	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs7643614	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7644725	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7649116	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653157	0.87[TSI][hapmap]
rs877142	1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]

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	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1005522	chr3:140454632-140685915	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536732	chr3:140454632-140685915	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv521218	chr3:140643038-140665147	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140641200-140644400	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr3:140641600-140646800	Weak transcription	Pancreas	Pancrea
3	chr3:140642000-140644400	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:140643000-140643800	Enhancers	Adipose Nuclei	Adipose
5	chr3:140643000-140643800	Enhancers	Psoas Muscle	Psoas
6	chr3:140643200-140644200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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