Variant report

Variant	rs11868098
Chromosome Location	chr17:46570869-46570870
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46568685..46570931-chr17:46575612..46578799,3	MCF-7	breast:
2	chr17:46569342..46572136-chr17:46582152..46585021,2	MCF-7	breast:
3	chr17:46569189..46572269-chr17:46574424..46577287,4	MCF-7	breast:
4	chr17:46568782..46571366-chr17:46604713..46607657,2	MCF-7	breast:
5	chr17:46570087..46572342-chr20:55574944..55576592,2	MCF-7	breast:
6	chr17:46570235..46572365-chr20:55509370..55511788,2	MCF-7	breast:
7	chr17:46569196..46571892-chr17:46596978..46599661,2	K562	blood:

Variant related genes	Relation type
ENSG00000251772	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1022088	0.86[ASN][1000 genomes]
rs1042818	0.86[EUR][1000 genomes]
rs1042822	0.86[EUR][1000 genomes]
rs12602539	0.87[EUR][1000 genomes]
rs12603976	0.87[EUR][1000 genomes]
rs12938390	0.87[EUR][1000 genomes]
rs12939811	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	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2229302	0.87[EUR][1000 genomes]
rs2326012	0.87[EUR][1000 genomes]
rs34378400	0.97[EUR][1000 genomes]
rs35621842	0.92[EUR][1000 genomes]
rs4239210	0.81[ASN][1000 genomes]
rs4793854	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793870	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4793889	0.88[AFR][1000 genomes];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	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504340	0.84[EUR][1000 genomes]
rs7207109	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	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8072250	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073963	0.85[EUR][1000 genomes]
rs8074125	0.88[EUR][1000 genomes]
rs8079617	0.89[EUR][1000 genomes]
rs9904760	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905940	0.84[EUR][1000 genomes]
rs9906950	0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11868098	HOXB-AS1	cis	Whole Blood	GTEx
rs11868098	HOXB2	cis	Whole Blood	GTEx
rs11868098	HOXB2	cis	Muscle Skeletal	GTEx
rs11868098	HOXB2	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46569600-46571000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:46569800-46571200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:46569800-46571600	Enhancers	Lung	lung
4	chr17:46570400-46571000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:46570400-46571000	Enhancers	Colon Smooth Muscle	Colon
6	chr17:46570400-46571000	Enhancers	NHDF-Ad	bronchial
7	chr17:46570400-46571600	Bivalent Enhancer	Fetal Lung	lung
8	chr17:46570400-46571600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr17:46570400-46571800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:46570400-46572400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr17:46570400-46572600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr17:46570400-46576400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:46570600-46571000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr17:46570600-46571000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr17:46570600-46571000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:46570600-46571000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr17:46570600-46571000	Enhancers	Primary hematopoietic stem cells	blood
18	chr17:46570600-46571000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:46570600-46571000	Enhancers	Fetal Kidney	kidney
20	chr17:46570600-46571000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr17:46570600-46571000	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr17:46570600-46571000	Bivalent Enhancer	Placenta	Placenta
23	chr17:46570600-46571000	Bivalent Enhancer	Rectal Smooth Muscle	rectum
24	chr17:46570600-46571400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr17:46570600-46571600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:46570600-46571600	Weak transcription	Osteobl	bone
27	chr17:46570600-46571800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:46570600-46572000	Enhancers	A549	lung
29	chr17:46570600-46572200	Enhancers	NHEK	skin
30	chr17:46570600-46572400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:46570600-46572400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:46570600-46572400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:46570600-46572400	Enhancers	HSMM	muscle
34	chr17:46570600-46572400	Enhancers	HSMMtube	muscle
35	chr17:46570600-46572400	Enhancers	NH-A	brain
36	chr17:46570600-46572400	Enhancers	NHLF	lung
37	chr17:46570600-46574200	Weak transcription	HMEC	breast
38	chr17:46570600-46574200	Weak transcription	HUVEC	blood vessel
39	chr17:46570600-46574800	Enhancers	K562	blood
40	chr17:46570800-46571000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
41	chr17:46570800-46571000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr17:46570800-46571000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:46570800-46571000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr17:46570800-46571200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
45	chr17:46570800-46571200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr17:46570800-46571200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr17:46570800-46571600	Weak transcription	Spleen	Spleen
48	chr17:46570800-46572400	Enhancers	Fetal Stomach	stomach
49	chr17:46570800-46574200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr17:46570800-46575000	Weak transcription	Adipose Nuclei	Adipose

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