Variant report

Variant	rs261968
Chromosome Location	chr5:95861029-95861030
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	chr5:95860896..95864045-chr5:95864403..95867369,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAST-1	chr5:95860971-95861131	XLOC_004480

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11135468	0.83[EUR][1000 genomes]
rs11135469	0.83[EUR][1000 genomes]
rs11742038	0.83[EUR][1000 genomes]
rs11742044	0.84[EUR][1000 genomes]
rs11742063	0.84[EUR][1000 genomes]
rs11948144	0.84[EUR][1000 genomes]
rs11959061	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13173434	0.83[EUR][1000 genomes]
rs13175874	0.82[ASN][1000 genomes]
rs13177618	0.83[EUR][1000 genomes]
rs13184161	0.84[EUR][1000 genomes]
rs13358815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1380500	0.83[EUR][1000 genomes]
rs1380501	0.83[EUR][1000 genomes]
rs156005	0.81[ASN][1000 genomes]
rs166374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1824425	0.83[EUR][1000 genomes]
rs1946628	0.89[EUR][1000 genomes]
rs195805	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2060352	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2117144	0.83[EUR][1000 genomes]
rs2117145	0.83[EUR][1000 genomes]
rs2163963	0.88[EUR][1000 genomes]
rs2217718	0.83[EUR][1000 genomes]
rs2350241	0.83[EUR][1000 genomes]
rs2570467	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570469	0.84[EUR][1000 genomes]
rs2578698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2611738	0.84[EUR][1000 genomes]
rs261961	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs261962	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs261963	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs261972	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs261973	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs261974	0.83[EUR][1000 genomes]
rs261978	0.84[EUR][1000 genomes]
rs261979	0.84[EUR][1000 genomes]
rs261980	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs261984	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs261985	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs261986	0.94[ASN][1000 genomes]
rs261988	0.93[ASN][1000 genomes]
rs263350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35057722	0.84[EUR][1000 genomes]
rs35190022	0.84[EUR][1000 genomes]
rs35283841	0.84[EUR][1000 genomes]
rs35809511	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4267885	0.83[EUR][1000 genomes]
rs4634375	0.83[EUR][1000 genomes]
rs4869143	0.83[EUR][1000 genomes]
rs4869144	0.83[EUR][1000 genomes]
rs4869290	0.83[EUR][1000 genomes]
rs62365724	0.85[EUR][1000 genomes]
rs6556928	0.82[EUR][1000 genomes]
rs6859191	0.82[EUR][1000 genomes]
rs6867933	0.83[EUR][1000 genomes]
rs6870000	0.82[EUR][1000 genomes]
rs6870152	0.82[EUR][1000 genomes]
rs6873005	0.83[EUR][1000 genomes]
rs6877870	0.83[EUR][1000 genomes]
rs6878046	0.83[EUR][1000 genomes]
rs6878234	0.83[EUR][1000 genomes]
rs6889388	0.84[EUR][1000 genomes]
rs71580786	0.81[EUR][1000 genomes]
rs7713454	0.84[EUR][1000 genomes]
rs7714425	0.84[EUR][1000 genomes]
rs7725914	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734121	0.84[EUR][1000 genomes]
rs7734417	0.84[EUR][1000 genomes]
rs7736659	0.84[EUR][1000 genomes]

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	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1026484	chr5:95759910-95961518	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr5:95857200-95864000	Weak transcription	Pancreas	Pancrea
2	chr5:95859200-95863600	Weak transcription	Hela-S3	cervix
3	chr5:95861000-95861200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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