Variant report

Variant	rs12568409
Chromosome Location	chr1:174079296-174079297
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	chr1:173835673..173838237-chr1:174076539..174080354,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10798302	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10912719	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10912722	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12076799	0.86[EUR][1000 genomes]
rs12092774	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12096785	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12563395	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13376011	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4592301	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61547493	0.82[ASN][1000 genomes]
rs61826843	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61826844	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827891	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827894	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6425273	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425275	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661868	0.97[ASN][1000 genomes]
rs6665484	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6673632	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6677660	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6689285	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6695327	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696163	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs714624	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7511780	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7538312	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7554915	0.85[EUR][1000 genomes];0.87[ASN][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	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 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	chr1:174078200-174079600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:174078800-174079600	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:174079000-174079800	Enhancers	GM12878-XiMat	blood

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