Variant report

Variant	rs8079617
Chromosome Location	chr17:46610028-46610029
allele	G/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	NR2F2	chr17:46609602-46610168	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46609132..46612079-chr17:46620945..46623382,2	MCF-7	breast:
2	chr17:46598935..46600877-chr17:46608428..46610318,2	MCF-7	breast:
3	chr17:46601060..46603214-chr17:46608437..46610558,2	MCF-7	breast:

Variant related genes	Relation type
HOXB1	TF binding region
ENSG00000230148	Chromatin interaction
ENSG00000173917	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1042818	0.97[EUR][1000 genomes]
rs1042822	0.97[EUR][1000 genomes]
rs1123630	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs11868098	0.89[EUR][1000 genomes]
rs12602539	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12603976	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12938390	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12939811	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];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12946855	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946931	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12947405	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12951076	0.95[EUR][1000 genomes]
rs12952262	1.00[JPT][hapmap]
rs1529334	1.00[JPT][hapmap]
rs17703636	0.88[EUR][1000 genomes]
rs17703660	0.88[EUR][1000 genomes]
rs2202895	0.84[EUR][1000 genomes]
rs2229302	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2326012	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34378400	0.92[EUR][1000 genomes]
rs35621842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646993	1.00[JPT][hapmap]
rs4793854	0.82[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4793889	0.91[EUR][1000 genomes]
rs4793943	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs55859232	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56038617	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56115209	0.94[EUR][1000 genomes]
rs56128659	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62065846	0.93[EUR][1000 genomes]
rs62066689	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066693	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6504281	0.81[EUR][1000 genomes]
rs6504340	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7207109	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207171	0.81[EUR][1000 genomes]
rs7222242	0.88[EUR][1000 genomes]
rs7225995	0.93[EUR][1000 genomes]
rs8064626	0.88[EUR][1000 genomes]
rs8066613	0.92[EUR][1000 genomes]
rs8071207	0.85[EUR][1000 genomes]
rs8072250	0.93[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs8073963	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872760	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs9904760	0.93[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs9905940	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9906950	0.85[EUR][1000 genomes]
rs9909884	1.00[JPT][hapmap]
rs9912500	1.00[JPT][hapmap]
rs9989493	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs8079617	HOXB2	cis	Adipose Subcutaneous	GTEx
rs8079617	HOXB2	cis	multi-tissue	Pritchard
rs8079617	PNPO	cis	parietal	SCAN
rs8079617	KLHL11	cis	cerebellum	SCAN
rs8079617	HOXB2	cis	uninvolved skin	skin_eQTL
rs8079617	HOXB2	cis	lung	GTEx
rs8079617	HOXB2	cis	Liver	GTEx
rs8079617	NBR1	cis	parietal	SCAN
rs8079617	HOXB-AS1	cis	Whole Blood	GTEx
rs8079617	PYY	cis	parietal	SCAN
rs8079617	HOXB2	cis	Whole Blood	GTEx
rs8079617	HOXB2	cis	cerebellum	SCAN
rs8079617	PNPO	cis	cerebellum	SCAN
rs8079617	LOC100130581	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46605200-46613000	Weak transcription	NHLF	lung
2	chr17:46606600-46610600	Weak transcription	HSMMtube	muscle
3	chr17:46608800-46611000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
4	chr17:46609000-46610400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:46609000-46611400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
6	chr17:46609200-46610200	Enhancers	A549	lung
7	chr17:46609400-46610200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
8	chr17:46609400-46610600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:46609800-46610200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:46609800-46611000	Enhancers	K562	blood
11	chr17:46610000-46610400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell

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