Variant report

Variant	rs230970
Chromosome Location	chr17:15264790-15264791
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	chr17:15254328..15256022-chr17:15263250..15265802,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12937472	0.86[ASN][1000 genomes]
rs230888	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs230889	0.84[JPT][hapmap];0.90[MEX][hapmap]
rs230901	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap]
rs230903	0.88[ASN][1000 genomes]
rs230904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs230906	0.88[ASN][1000 genomes]
rs230907	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs230909	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs230910	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs230977	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2531955	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs2875118	0.82[ASN][1000 genomes]
rs34174662	0.82[ASN][1000 genomes]
rs36023606	0.82[ASN][1000 genomes]
rs364785	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs372882	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs394106	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs395945	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs396445	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs396895	0.88[ASN][1000 genomes]
rs399666	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs401664	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs406112	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs414494	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs417637	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs427476	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs427531	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs433068	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs433993	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs446597	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs450848	0.88[ASN][1000 genomes]
rs561167	0.88[ASN][1000 genomes]
rs609537	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription 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	22 gene(s)	inside rSNPs	diseases
2	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv907703	chr17:15199907-15370701	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs230970	LOC162632	cis	parietal	SCAN
rs230970	COX10	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15264200-15265400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr17:15264400-15265000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr17:15264600-15264800	Enhancers	K562	blood

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