Variant report

Variant	rs269868
Chromosome Location	chr15:45392075-45392076
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	chr15:45377878..45380609-chr15:45390291..45392505,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10851420	0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[ASN][1000 genomes]
rs1108085	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12441189	0.82[CHB][hapmap]
rs166574	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs175088	0.92[MEX][hapmap]
rs190599	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1961660	1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs199138	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001616	0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs2002813	1.00[JPT][hapmap]
rs2252371	0.90[ASW][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs2437866	0.82[CHB][hapmap]
rs2470686	0.82[CHB][hapmap]
rs2554451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576092	1.00[MEX][hapmap]
rs269856	1.00[MEX][hapmap]
rs269859	0.85[JPT][hapmap];0.92[MEX][hapmap];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs269862	0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs269863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269866	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs28488149	0.94[ASN][1000 genomes]
rs28662287	0.80[ASW][hapmap]
rs3743222	1.00[JPT][hapmap]
rs4775744	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs56833067	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56838826	0.82[EUR][1000 genomes]
rs57659670	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61626661	0.82[EUR][1000 genomes]
rs6493131	0.82[CHB][hapmap]
rs7171366	1.00[JPT][hapmap]
rs7180106	1.00[JPT][hapmap]
rs7180976	0.87[ASN][1000 genomes]
rs7183046	1.00[JPT][hapmap]
rs73406330	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73406334	0.82[EUR][1000 genomes]
rs73406335	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73406337	0.80[EUR][1000 genomes]
rs8024922	0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs953733	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs955152	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv457124	chr15:45381998-45460422	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv569312	chr15:45381998-45460422	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs269868	SORD	cis	multi-tissue	Pritchard
rs269868	CTD-2008A1.1	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45363800-45398400	Weak transcription	Gastric	stomach
2	chr15:45381400-45404600	Weak transcription	Right Atrium	heart
3	chr15:45383400-45395200	Weak transcription	Colonic Mucosa	Colon
4	chr15:45387400-45393200	Weak transcription	Right Ventricle	heart
5	chr15:45391600-45395200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:45391800-45392400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:45392000-45394000	Weak transcription	Esophagus	oesophagus

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