Variant report

Variant	rs9904760
Chromosome Location	chr17:46575031-46575032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46574039..46576397-chr17:46577646..46580624,4	MCF-7	breast:
2	chr17:46553956..46556675-chr17:46573169..46576403,3	MCF-7	breast:
3	chr17:46569189..46572269-chr17:46574424..46577287,4	MCF-7	breast:
4	chr17:46572156..46575042-chr17:46583182..46586038,3	MCF-7	breast:
5	chr17:46574929..46577618-chr17:46713950..46715500,2	K562	blood:
6	chr17:46573441..46575512-chr17:46598331..46600721,2	MCF-7	breast:
7	chr17:46574112..46575706-chr17:46580959..46582706,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206805	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1022088	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1042818	0.86[EUR][1000 genomes]
rs1042822	0.86[EUR][1000 genomes]
rs11868098	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602539	0.87[EUR][1000 genomes]
rs12603976	0.87[EUR][1000 genomes]
rs12938390	0.87[EUR][1000 genomes]
rs12939811	0.93[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs12946855	0.85[EUR][1000 genomes]
rs12946931	0.87[EUR][1000 genomes]
rs12947405	0.87[EUR][1000 genomes]
rs12951076	0.84[EUR][1000 genomes]
rs17703636	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17703660	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2202895	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2229302	0.93[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2326012	0.87[EUR][1000 genomes]
rs34378400	0.97[EUR][1000 genomes]
rs35621842	0.93[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs4239210	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4793854	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]
rs4793870	0.83[ASN][1000 genomes]
rs4793889	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4794733	0.81[ASN][1000 genomes]
rs55859232	0.89[EUR][1000 genomes]
rs56038617	0.89[EUR][1000 genomes]
rs56115209	0.83[EUR][1000 genomes]
rs56128659	0.87[EUR][1000 genomes]
rs62065846	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62066689	0.90[EUR][1000 genomes]
rs62066693	0.87[EUR][1000 genomes]
rs6504281	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504340	0.81[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7207109	0.81[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7207171	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7222242	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7225995	0.96[EUR][1000 genomes]
rs8064626	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8066613	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8071207	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8072250	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];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073963	0.81[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs8074125	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs8079617	0.93[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs9905940	0.84[EUR][1000 genomes]
rs9906950	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9989493	0.96[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9904760	HOXB2	cis	uninvolved skin	skin_eQTL
rs9904760	KLHL11	cis	cerebellum	SCAN
rs9904760	HOXB-AS1	cis	Whole Blood	GTEx
rs9904760	HOXB2	cis	cerebellum	SCAN
rs9904760	HOXB2	cis	Whole Blood	GTEx
rs9904760	HOXB2	cis	multi-tissue	Pritchard
rs9904760	JUP	cis	cerebellum	SCAN
rs9904760	PNPO	cis	parietal	SCAN
rs9904760	LOC100130581	cis	parietal	SCAN
rs9904760	NBR1	cis	parietal	SCAN
rs9904760	PYY	cis	parietal	SCAN
rs9904760	PNPO	cis	cerebellum	SCAN
rs9904760	HOXB2	cis	Muscle Skeletal	GTEx
rs9904760	HOXB2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46570400-46576400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:46571000-46577800	Weak transcription	Colon Smooth Muscle	Colon
3	chr17:46571200-46575400	Weak transcription	Placenta	Placenta
4	chr17:46571800-46575800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr17:46572600-46575600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr17:46573200-46577200	Weak transcription	A549	lung
7	chr17:46573400-46576400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr17:46574000-46576600	Enhancers	Fetal Stomach	stomach
9	chr17:46574200-46575200	Enhancers	NH-A	brain
10	chr17:46574200-46575800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr17:46574200-46575800	Enhancers	NHLF	lung
12	chr17:46574200-46576200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr17:46574200-46576200	Enhancers	Fetal Kidney	kidney
14	chr17:46574200-46576400	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr17:46574200-46576400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr17:46574200-46576800	Enhancers	NHEK	skin
17	chr17:46574200-46577800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:46574200-46578400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr17:46574200-46578600	Enhancers	HSMM	muscle
20	chr17:46574200-46579400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:46574400-46577000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr17:46574600-46588000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:46574800-46576400	Enhancers	HSMMtube	muscle
24	chr17:46574800-46577400	Weak transcription	K562	blood
25	chr17:46574800-46582800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr17:46574800-46582800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:46574800-46582800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr17:46575000-46575800	Enhancers	Adipose Nuclei	Adipose
29	chr17:46575000-46575800	Bivalent Enhancer	Fetal Lung	lung

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