Variant report

Variant	rs230907
Chromosome Location	chr17:15236022-15236023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr17:15235646-15236107	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3A	chr17:15235658-15236163	H1-hESC	embryonic stem cell:	n/a	n/a
3	EP300	chr17:15235597-15236090	H1-hESC	embryonic stem cell:	n/a	n/a
4	POU5F1	chr17:15235715-15236142	H1-hESC	embryonic stem cell:	n/a	n/a
5	TEAD4	chr17:15235616-15236059	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr17:15235675-15236052	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr17:15235544-15236052	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr17:15235663-15236115	H1-hESC	embryonic stem cell:	n/a	chr17:15235827-15235838
9	SP1	chr17:15235558-15236161	H1-hESC	embryonic stem cell:	n/a	chr17:15235827-15235838
10	JUND	chr17:15235638-15236169	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD2	chr17:15235597-15236106	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15235028..15236798-chr20:46132185..46133884,2	MCF-7	breast:

Variant related genes	Relation type
TEKT3	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12937472	0.82[ASN][1000 genomes]
rs16951395	0.85[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs230888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230889	1.00[ASW][hapmap];0.90[CEU][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs230892	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230903	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230904	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230905	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs230906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230970	0.88[ASN][1000 genomes]
rs230977	0.89[ASN][1000 genomes]
rs2531955	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs364785	0.97[ASN][1000 genomes]
rs372882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs394106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs396445	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs396895	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs401664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs406112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450848	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561167	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609537	0.85[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs230907	COX10	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15235600-15236200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr17:15235600-15236200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr17:15235600-15236600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:15235600-15236800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr17:15235800-15236200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr17:15235800-15236400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr17:15235800-15236600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr17:15236000-15236200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr17:15236000-15236200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr17:15236000-15236400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr17:15236000-15236400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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