Variant report

Variant	rs1107233
Chromosome Location	chr5:60020520-60020521
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	chr5:59994985..59997497-chr5:60017643..60020875,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000035499	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10073959	0.86[ASN][1000 genomes]
rs1026418	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs1107232	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12658660	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1379111	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs1379113	0.81[ASN][1000 genomes]
rs1456744	0.86[ASN][1000 genomes]
rs1460959	0.93[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs1563516	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1563517	0.93[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs1563518	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs1563519	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs1563520	0.86[ASN][1000 genomes]
rs1563521	0.86[ASN][1000 genomes]
rs1563905	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs1563906	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs1563907	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs16878315	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs16878354	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16878411	0.95[ASN][1000 genomes]
rs16878412	0.86[ASN][1000 genomes]
rs16878413	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1870012	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1870013	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1982595	0.86[ASN][1000 genomes]
rs1982596	0.86[ASN][1000 genomes]
rs1992613	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs2045355	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs2124751	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs2169254	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs2305680	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2898298	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs34915115	0.81[ASN][1000 genomes]
rs3857238	0.93[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs4273559	0.93[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs4565168	0.86[ASN][1000 genomes]
rs4623105	0.86[ASN][1000 genomes]
rs6871928	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs6885202	0.95[ASN][1000 genomes]
rs6885787	0.86[ASN][1000 genomes]
rs7701983	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7702459	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs7706896	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs7708849	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs7712043	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs7713586	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7713673	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7716051	0.93[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs7719525	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7733069	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs881066	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs897671	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs897673	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	esv2763456	chr5:60007355-60151767	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv1026190	chr5:60020156-60148535	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv537769	chr5:60020156-60148535	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 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	chr5:60020200-60032800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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