Variant report

Variant	rs8072250
Chromosome Location	chr17:46569216-46569217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46563248..46569374-chr17:46695616..46701359,7	K562	blood:
2	chr17:46569144..46570490-chr17:46662375..46663400,6	MCF-7	breast:
3	chr17:46568685..46570931-chr17:46575612..46578799,3	MCF-7	breast:
4	chr17:46569189..46572269-chr17:46574424..46577287,4	MCF-7	breast:
5	chr17:46568782..46571366-chr17:46604713..46607657,2	MCF-7	breast:
6	chr17:46568691..46570864-chr17:46669281..46671058,2	K562	blood:
7	chr17:46568059..46570366-chr17:46679514..46681666,2	K562	blood:
8	chr17:46532115..46533858-chr17:46568103..46570537,2	MCF-7	breast:
9	chr17:46566753..46569471-chr17:46581683..46584279,2	MCF-7	breast:
10	chr17:46564020..46565955-chr17:46568575..46570721,2	K562	blood:
11	chr17:46569196..46571892-chr17:46596978..46599661,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000233101	Chromatin interaction
ENSG00000108511	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	0.83[EUR][1000 genomes]
rs1042822	0.83[EUR][1000 genomes]
rs11868098	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602539	0.85[EUR][1000 genomes]
rs12603976	0.84[EUR][1000 genomes]
rs12938390	0.85[EUR][1000 genomes]
rs12939811	0.93[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs12946855	0.83[EUR][1000 genomes]
rs12946931	0.85[EUR][1000 genomes]
rs12947405	0.85[EUR][1000 genomes]
rs12951076	0.82[EUR][1000 genomes]
rs17703636	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17703660	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2202895	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2229302	0.93[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2326012	0.85[EUR][1000 genomes]
rs34378400	0.94[EUR][1000 genomes]
rs35621842	0.93[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs4239210	0.83[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];0.83[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793870	0.83[ASN][1000 genomes]
rs4793889	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4794733	0.81[ASN][1000 genomes]
rs55859232	0.86[EUR][1000 genomes]
rs56038617	0.86[EUR][1000 genomes]
rs56115209	0.81[EUR][1000 genomes]
rs56128659	0.85[EUR][1000 genomes]
rs62065846	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62066689	0.88[EUR][1000 genomes]
rs62066693	0.85[EUR][1000 genomes]
rs6504281	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504340	0.81[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7207109	0.81[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7207171	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7222242	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7225995	0.94[EUR][1000 genomes]
rs8064626	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8066613	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8071207	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8073963	0.81[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs8074125	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs8079617	0.93[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs9904760	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]
rs9905940	0.82[EUR][1000 genomes]
rs9906950	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9989493	0.94[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
rs8072250	HOXB2	cis	Adipose Subcutaneous	GTEx
rs8072250	HOXB2	cis	Whole Blood	GTEx
rs8072250	KLHL11	cis	cerebellum	SCAN
rs8072250	JUP	cis	cerebellum	SCAN
rs8072250	NBR1	cis	parietal	SCAN
rs8072250	PYY	cis	parietal	SCAN
rs8072250	LOC100130581	cis	parietal	SCAN
rs8072250	HOXB2	cis	multi-tissue	Pritchard
rs8072250	PNPO	cis	parietal	SCAN
rs8072250	PNPO	cis	cerebellum	SCAN
rs8072250	HOXB2	cis	cerebellum	SCAN
rs8072250	HOXB-AS1	cis	Whole Blood	GTEx
rs8072250	HOXB2	cis	uninvolved skin	skin_eQTL
rs8072250	HOXB2	cis	Muscle Skeletal	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46561400-46569400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr17:46561400-46569600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:46562000-46569800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:46564600-46569400	Weak transcription	A549	lung
5	chr17:46564600-46569800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:46564600-46569800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:46564600-46569800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:46564800-46569800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr17:46564800-46569800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:46564800-46569800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr17:46565000-46569400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:46565000-46569800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:46565000-46569800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr17:46565000-46569800	Weak transcription	NHDF-Ad	bronchial
15	chr17:46565600-46569800	Enhancers	Primary hematopoietic stem cells	blood
16	chr17:46566200-46569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:46566400-46569800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr17:46566400-46569800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr17:46566400-46569800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:46566400-46569800	Weak transcription	Gastric	stomach
21	chr17:46566400-46569800	Weak transcription	HMEC	breast
22	chr17:46566600-46569400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr17:46566600-46569400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr17:46567800-46569800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr17:46567800-46569800	Enhancers	Placenta	Placenta
26	chr17:46568000-46569600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:46568000-46569600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr17:46568000-46569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:46568200-46569800	Weak transcription	NH-A	brain
30	chr17:46568400-46569800	Enhancers	Adipose Nuclei	Adipose
31	chr17:46568400-46569800	Weak transcription	Colon Smooth Muscle	Colon
32	chr17:46568400-46569800	Weak transcription	HSMMtube	muscle
33	chr17:46568600-46569600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr17:46568600-46569800	Weak transcription	NHEK	skin
35	chr17:46568800-46569800	Weak transcription	Psoas Muscle	Psoas
36	chr17:46568800-46569800	Enhancers	HUVEC	blood vessel
37	chr17:46569000-46569400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
38	chr17:46569000-46569800	Enhancers	Primary B cells from cord blood	blood
39	chr17:46569000-46569800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr17:46569000-46569800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr17:46569000-46569800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr17:46569000-46569800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr17:46569000-46569800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr17:46569000-46569800	Enhancers	Fetal Stomach	stomach
45	chr17:46569200-46569600	Flanking Active TSS	GM12878-XiMat	blood
46	chr17:46569200-46569600	Enhancers	HSMM	muscle
47	chr17:46569200-46569800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
48	chr17:46569200-46569800	Enhancers	Primary T cells from cord blood	blood
49	chr17:46569200-46569800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:46569200-46569800	Enhancers	Fetal Kidney	kidney

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