Variant report

Variant	rs12952262
Chromosome Location	chr17:46683800-46683801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr17:46683726-46683951	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr17:46683419-46684861	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
4	CTBP2	chr17:46683262-46683909	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr17:46683406-46683809	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr17:46683702-46684302	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr17:46683789-46684333	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46622432..46624034-chr17:46681830..46683830,2	K562	blood:
2	chr17:46675371..46683952-chr17:46685648..46690575,16	MCF-7	breast:
3	chr17:46679267..46681075-chr17:46682371..46684611,3	MCF-7	breast:

No data

Variant related genes	Relation type
HOXB6	TF binding region
HOXB3	TF binding region
ENSG00000260027	Chromatin interaction
ENSG00000233101	Chromatin interaction
ENSG00000173917	Chromatin interaction
ENSG00000230148	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1123630	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12939324	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12939811	1.00[JPT][hapmap]
rs1529334	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2229302	1.00[JPT][hapmap]
rs28575348	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4239158	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs4646993	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4793589	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4793938	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4793939	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4793943	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4793951	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62064564	0.80[EUR][1000 genomes]
rs6504340	1.00[JPT][hapmap]
rs66459980	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7207109	1.00[JPT][hapmap]
rs8073963	1.00[JPT][hapmap]
rs8074125	1.00[JPT][hapmap]
rs8079617	1.00[JPT][hapmap]
rs872760	1.00[ASW][hapmap];0.87[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9896015	0.91[EUR][1000 genomes]
rs9909884	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9912500	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS 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	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised 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	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription 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	349 gene(s)	inside rSNPs	diseases
11	nsv575480	chr17:46617019-46684929	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	nsv908582	chr17:46617019-46698710	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	nsv908583	chr17:46617019-46704536	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
14	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers 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	356 gene(s)	inside rSNPs	diseases
15	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
16	nsv457822	chr17:46620402-46698710	Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
17	nsv575481	chr17:46620402-46698710	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription 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	334 gene(s)	inside rSNPs	diseases
18	nsv457823	chr17:46620402-46704536	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
19	nsv575482	chr17:46620402-46704536	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
20	nsv457824	chr17:46625519-46693491	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription 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	332 gene(s)	inside rSNPs	diseases
21	nsv575483	chr17:46625519-46693491	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12952262	HOXB2	cis	Whole Blood	GTEx
rs12952262	HOXB2	cis	Adipose Subcutaneous	GTEx
rs12952262	PNPO	cis	parietal	SCAN
rs12952262	SLC35B1	cis	cerebellum	SCAN
rs12952262	CNP	cis	parietal	SCAN
rs12952262	HOXB2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46677400-46684000	Active TSS	Fetal Kidney	kidney
2	chr17:46681200-46686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr17:46681800-46684600	Active TSS	Colonic Mucosa	Colon
4	chr17:46681800-46686400	Weak transcription	GM12878-XiMat	blood
5	chr17:46682400-46684400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:46682800-46686600	Weak transcription	HSMMtube	muscle
7	chr17:46683000-46683800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr17:46683000-46683800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr17:46683000-46684000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr17:46683000-46684000	Enhancers	NHDF-Ad	bronchial
11	chr17:46683000-46686400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr17:46683000-46686600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:46683000-46686600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:46683200-46684000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:46683200-46684000	Enhancers	Adipose Nuclei	Adipose
16	chr17:46683200-46684000	Weak transcription	HSMM	muscle
17	chr17:46683200-46684000	Enhancers	HUVEC	blood vessel
18	chr17:46683200-46684200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:46683200-46684200	Weak transcription	Colon Smooth Muscle	Colon
20	chr17:46683200-46685800	Weak transcription	K562	blood
21	chr17:46683200-46686200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr17:46683400-46683800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
23	chr17:46683400-46684000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr17:46683400-46684000	Weak transcription	A549	lung
25	chr17:46683400-46685400	Strong transcription	NHLF	lung
26	chr17:46683600-46683800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:46683600-46683800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr17:46683600-46683800	Enhancers	Hela-S3	cervix
29	chr17:46683600-46684000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr17:46683600-46684200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:46683600-46691000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr17:46683800-46684000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
33	chr17:46683800-46684000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:46683800-46684000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
35	chr17:46683800-46684000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:46683800-46684000	Bivalent Enhancer	Fetal Intestine Large	intestine
37	chr17:46683800-46684000	Flanking Active TSS	Hela-S3	cervix
38	chr17:46683800-46684200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:46683800-46684600	Strong transcription	Rectal Smooth Muscle	rectum
40	chr17:46683800-46685400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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