Variant report

Variant	rs3006414
Chromosome Location	chr1:153391729-153391730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153327790..153331196-chr1:153389246..153391874,3	MCF-7	breast:
2	chr1:153334094..153336185-chr1:153390853..153392879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10127752	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888560	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs11205297	0.90[GIH][hapmap]
rs12022550	0.88[CHB][hapmap]
rs12036701	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12043280	0.88[GIH][hapmap]
rs12043556	0.82[CHB][hapmap]
rs12047494	0.80[CHB][hapmap]
rs16835308	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs16835332	0.80[CHB][hapmap]
rs2986209	0.80[CHB][hapmap]
rs3006412	0.90[CHB][hapmap]
rs3006413	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3006416	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3006422	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3006423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3014813	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3014814	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3014815	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3014816	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3014817	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3014818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3014822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3014823	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs3014848	0.84[CHB][hapmap]
rs4507965	0.88[ASN][1000 genomes]
rs4845348	1.00[CHB][hapmap]

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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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