Variant report

Variant	rs8074125
Chromosome Location	chr17:46610060-46610061
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
ENSG00000173917	Chromatin interaction
ENSG00000230148	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1042818	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1042822	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1123630	1.00[JPT][hapmap]
rs11868098	0.88[EUR][1000 genomes]
rs12602539	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12603976	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12938390	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12939811	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];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12946855	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946931	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12947405	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12951076	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12952262	1.00[JPT][hapmap]
rs1529334	1.00[JPT][hapmap]
rs17703636	0.87[EUR][1000 genomes]
rs17703660	0.87[EUR][1000 genomes]
rs2202895	0.83[EUR][1000 genomes]
rs2229302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];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	0.91[EUR][1000 genomes]
rs35621842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646993	1.00[JPT][hapmap]
rs4793854	0.83[EUR][1000 genomes]
rs4793889	0.90[EUR][1000 genomes]
rs4793943	1.00[JPT][hapmap]
rs55859232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56038617	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56115209	0.93[EUR][1000 genomes]
rs56128659	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62065846	0.92[EUR][1000 genomes]
rs62066689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066693	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6504281	0.80[EUR][1000 genomes]
rs6504340	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7207109	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207171	0.81[EUR][1000 genomes]
rs7222242	0.87[EUR][1000 genomes]
rs7225995	0.92[EUR][1000 genomes]
rs8064626	0.87[EUR][1000 genomes]
rs8066613	0.91[EUR][1000 genomes]
rs8071207	0.85[EUR][1000 genomes]
rs8072250	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs8073963	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079617	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	1.00[JPT][hapmap]
rs9904760	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs9905940	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9906950	0.84[EUR][1000 genomes]
rs9909884	1.00[JPT][hapmap]
rs9912500	1.00[JPT][hapmap]
rs9989493	0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8074125	HOXB2	cis	lung	GTEx
rs8074125	HOXB2	cis	Whole Blood	GTEx
rs8074125	HOXB2	cis	uninvolved skin	skin_eQTL
rs8074125	HOXB2	cis	Adipose Subcutaneous	GTEx
rs8074125	HOXB-AS1	cis	Whole Blood	GTEx

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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