Variant report

Variant	rs4793854
Chromosome Location	chr17:46572133-46572134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46569342..46572136-chr17:46582152..46585021,2	MCF-7	breast:
2	chr17:46569189..46572269-chr17:46574424..46577287,4	MCF-7	breast:
3	chr17:46570087..46572342-chr20:55574944..55576592,2	MCF-7	breast:
4	chr17:46570235..46572365-chr20:55509370..55511788,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251772	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1022088	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1042818	0.81[EUR][1000 genomes]
rs1042822	0.81[EUR][1000 genomes]
rs11868098	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602539	0.82[EUR][1000 genomes]
rs12603976	0.82[EUR][1000 genomes]
rs12938390	0.82[EUR][1000 genomes]
rs12939811	0.82[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12946855	0.91[EUR][1000 genomes]
rs12946931	0.82[EUR][1000 genomes]
rs12947405	0.82[EUR][1000 genomes]
rs17703636	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17703660	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2202895	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2229302	0.82[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2326012	0.82[EUR][1000 genomes]
rs34378400	0.92[EUR][1000 genomes]
rs35621842	0.82[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs4239210	0.81[ASN][1000 genomes]
rs4793870	0.83[ASN][1000 genomes]
rs4793889	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4794733	0.81[ASN][1000 genomes]
rs55859232	0.84[EUR][1000 genomes]
rs56038617	0.84[EUR][1000 genomes]
rs56128659	0.82[EUR][1000 genomes]
rs62065846	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62066689	0.85[EUR][1000 genomes]
rs62066693	0.82[EUR][1000 genomes]
rs6504281	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504340	0.94[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7207109	0.94[CEU][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs7207171	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7222242	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7225995	0.91[EUR][1000 genomes]
rs8064626	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8066613	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8071207	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8072250	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073963	0.94[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs8074125	0.83[EUR][1000 genomes]
rs8079617	0.82[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs9904760	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905940	0.89[EUR][1000 genomes]
rs9906950	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9989493	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv1002528	chr17:46566180-46575960	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4793854	HOXB2	cis	Adipose Subcutaneous	GTEx
rs4793854	HOXB2	Cis_1M	lymphoblastoid	RTeQTL
rs4793854	KLHL11	cis	cerebellum	SCAN
rs4793854	LOC100130581	cis	parietal	SCAN
rs4793854	HOXB2	cis	uninvolved skin	skin_eQTL
rs4793854	HOXB2	cis	Whole Blood	GTEx
rs4793854	HOXB-AS1	cis	Whole Blood	GTEx
rs4793854	JUP	cis	cerebellum	SCAN
rs4793854	HOXB2	cis	cerebellum	SCAN
rs4793854	PNPO	cis	parietal	SCAN
rs4793854	PYY	cis	parietal	SCAN
rs4793854	PNPO	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46570400-46572400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr17:46570400-46572600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr17:46570400-46576400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:46570600-46572200	Enhancers	NHEK	skin
5	chr17:46570600-46572400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr17:46570600-46572400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:46570600-46572400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:46570600-46572400	Enhancers	HSMM	muscle
9	chr17:46570600-46572400	Enhancers	HSMMtube	muscle
10	chr17:46570600-46572400	Enhancers	NH-A	brain
11	chr17:46570600-46572400	Enhancers	NHLF	lung
12	chr17:46570600-46574200	Weak transcription	HMEC	breast
13	chr17:46570600-46574200	Weak transcription	HUVEC	blood vessel
14	chr17:46570600-46574800	Enhancers	K562	blood
15	chr17:46570800-46572400	Enhancers	Fetal Stomach	stomach
16	chr17:46570800-46574200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:46570800-46575000	Weak transcription	Adipose Nuclei	Adipose
18	chr17:46571000-46574200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr17:46571000-46574400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:46571000-46577800	Weak transcription	Colon Smooth Muscle	Colon
21	chr17:46571200-46575400	Weak transcription	Placenta	Placenta
22	chr17:46571400-46572200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr17:46571400-46572200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:46571400-46572200	Enhancers	NHDF-Ad	bronchial
25	chr17:46571600-46572400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:46571600-46572400	Enhancers	Osteobl	bone
27	chr17:46571800-46572400	Bivalent Enhancer	Fetal Lung	lung
28	chr17:46571800-46574000	Weak transcription	Spleen	Spleen
29	chr17:46571800-46574200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr17:46571800-46574200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr17:46571800-46575800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr17:46572000-46572400	Flanking Active TSS	A549	lung
33	chr17:46572000-46573400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr17:46572000-46574200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr17:46572000-46574200	Weak transcription	Fetal Kidney	kidney

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