Variant report

Variant	rs6109825
Chromosome Location	chr20:1388068-1388069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1387186..1389098-chr20:1391471..1393677,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11087052	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs1884389	0.84[JPT][hapmap]
rs1998007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144542	0.85[ASN][1000 genomes]
rs2144543	0.85[ASN][1000 genomes]
rs2144545	0.84[JPT][hapmap]
rs2207828	0.94[ASN][1000 genomes]
rs2207829	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207830	0.86[ASN][1000 genomes]
rs3088080	0.84[JPT][hapmap]
rs36018423	0.85[ASN][1000 genomes]
rs3829698	0.88[JPT][hapmap]
rs4813133	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4814229	0.93[ASN][1000 genomes]
rs4814231	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814237	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4814240	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4814243	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4814244	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs5019244	0.85[ASN][1000 genomes]
rs6033691	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033697	0.93[ASN][1000 genomes]
rs6033698	0.93[ASN][1000 genomes]
rs6033707	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033709	0.93[ASN][1000 genomes]
rs6033710	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs6033715	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6033726	0.85[ASN][1000 genomes]
rs6033728	0.85[ASN][1000 genomes]
rs6033729	0.85[ASN][1000 genomes]
rs6033732	0.85[ASN][1000 genomes]
rs6033744	0.85[ASN][1000 genomes]
rs6033753	0.86[ASN][1000 genomes]
rs6033807	0.84[JPT][hapmap]
rs6042032	0.84[ASN][1000 genomes]
rs6042066	0.93[ASN][1000 genomes]
rs6042071	0.93[ASN][1000 genomes]
rs6042072	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042074	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042088	0.93[ASN][1000 genomes]
rs6042091	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042117	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6042118	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6042131	0.85[ASN][1000 genomes]
rs6042160	0.85[ASN][1000 genomes]
rs6042170	0.85[ASN][1000 genomes]
rs6042172	0.85[ASN][1000 genomes]
rs6042175	0.85[ASN][1000 genomes]
rs6042197	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6042207	0.85[ASN][1000 genomes]
rs6042208	0.85[ASN][1000 genomes]
rs6042209	0.81[ASN][1000 genomes]
rs6042270	0.84[JPT][hapmap]
rs6074593	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074623	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079010	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079013	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079133	0.83[JPT][hapmap]
rs6105076	0.84[ASN][1000 genomes]
rs6105079	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105081	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105102	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6105110	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6105165	0.84[JPT][hapmap]
rs6109893	0.85[ASN][1000 genomes]
rs6109894	0.85[ASN][1000 genomes]
rs6109912	0.85[ASN][1000 genomes]
rs6131468	0.93[ASN][1000 genomes]
rs6134916	0.85[ASN][1000 genomes]
rs6514382	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514383	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891	0.84[JPT][hapmap]
rs750424	0.85[ASN][1000 genomes]
rs8124053	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs873523	0.81[ASN][1000 genomes]
rs910619	0.84[JPT][hapmap]
rs926977	0.86[ASN][1000 genomes]
rs932524	0.84[JPT][hapmap]
rs9575	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv994443	chr20:1385239-1392933	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1819763	chr20:1386940-1390683	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv1834375	chr20:1386940-1390683	Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv1817885	chr20:1386940-1400227	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3453894	chr20:1387152-1392750	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv1815191	chr20:1387658-1390682	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	esv1819996	chr20:1387658-1390682	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv1835632	chr20:1387658-1390682	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	esv1841302	chr20:1387658-1390682	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	esv1847243	chr20:1387658-1390682	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	esv1849807	chr20:1387658-1390682	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	esv3497599	chr20:1387952-1391950	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1380600-1388400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr20:1382400-1388400	Weak transcription	Placenta	Placenta
3	chr20:1383800-1396000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:1384400-1395600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:1384400-1396000	Weak transcription	HMEC	breast

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