Variant report

Variant	rs9906950
Chromosome Location	chr17:46577167-46577168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46575874..46579148-chr17:46581240..46583659,4	MCF-7	breast:
2	chr17:46569189..46572269-chr17:46574424..46577287,4	MCF-7	breast:
3	chr17:46575342..46577434-chr17:46588645..46590527,2	K562	blood:
4	chr17:46568685..46570931-chr17:46575612..46578799,3	MCF-7	breast:
5	chr17:46574929..46577618-chr17:46713950..46715500,2	K562	blood:
6	chr17:46564497..46566146-chr17:46575665..46577794,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1022088	0.90[ASN][1000 genomes]
rs1042818	0.82[EUR][1000 genomes]
rs1042822	0.82[EUR][1000 genomes]
rs11868098	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12602539	0.83[EUR][1000 genomes]
rs12603976	0.82[EUR][1000 genomes]
rs12938390	0.83[EUR][1000 genomes]
rs12939811	0.86[EUR][1000 genomes]
rs12946855	0.91[EUR][1000 genomes]
rs12946931	0.83[EUR][1000 genomes]
rs12947405	0.83[EUR][1000 genomes]
rs12951076	0.80[EUR][1000 genomes]
rs17703636	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17703660	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2202895	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2229302	0.83[EUR][1000 genomes]
rs2326012	0.83[EUR][1000 genomes]
rs34378400	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35621842	0.88[EUR][1000 genomes]
rs4793854	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4793870	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4793889	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55859232	0.85[EUR][1000 genomes]
rs56038617	0.85[EUR][1000 genomes]
rs56128659	0.83[EUR][1000 genomes]
rs62065846	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62066689	0.86[EUR][1000 genomes]
rs62066693	0.83[EUR][1000 genomes]
rs6504281	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6504340	0.90[EUR][1000 genomes]
rs7207109	0.91[EUR][1000 genomes]
rs7207171	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7222242	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7225995	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8064626	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8066613	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8071207	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072250	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8073963	0.91[EUR][1000 genomes]
rs8074125	0.84[EUR][1000 genomes]
rs8079617	0.85[EUR][1000 genomes]
rs9904760	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9905940	0.90[EUR][1000 genomes]
rs9989493	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9906950	HOXB2	cis	Adipose Subcutaneous	GTEx
rs9906950	HOXB-AS1	cis	Whole Blood	GTEx
rs9906950	HOXB2	Cis_1M	lymphoblastoid	RTeQTL
rs9906950	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46571000-46577800	Weak transcription	Colon Smooth Muscle	Colon
2	chr17:46573200-46577200	Weak transcription	A549	lung
3	chr17:46574200-46577800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:46574200-46578400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr17:46574200-46578600	Enhancers	HSMM	muscle
6	chr17:46574200-46579400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:46574600-46588000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:46574800-46577400	Weak transcription	K562	blood
9	chr17:46574800-46582800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:46574800-46582800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:46574800-46582800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr17:46575400-46577200	Enhancers	Placenta	Placenta
13	chr17:46575800-46577600	Weak transcription	NHLF	lung
14	chr17:46576000-46577400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr17:46576200-46577200	Weak transcription	Fetal Kidney	kidney
16	chr17:46576200-46578000	Weak transcription	Fetal Lung	lung
17	chr17:46576400-46577200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr17:46576400-46577400	Weak transcription	HSMMtube	muscle
19	chr17:46576400-46577800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr17:46576400-46578400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr17:46576600-46577200	Weak transcription	Fetal Stomach	stomach
22	chr17:46576600-46579600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr17:46576800-46579200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr17:46576800-46582000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr17:46577000-46577200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr17:46577000-46577400	Enhancers	NHDF-Ad	bronchial
27	chr17:46577000-46578000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:46577000-46578800	Enhancers	NH-A	brain

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