Variant report

Variant	rs2288278
Chromosome Location	chr17:46661292-46661293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
2	JUN	chr17:46659711-46663371	K562	blood:	n/a	chr17:46660858-46660868 chr17:46662012-46662022 chr17:46662089-46662097 chr17:46662013-46662021 chr17:46662012-46662022 chr17:46660702-46660713
3	CHD1	chr17:46655927-46662288	IMR90	lung:	n/a	chr17:46657663-46657673 chr17:46660648-46660658
4	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46529355..46532196-chr17:46660157..46661823,2	K562	blood:
2	chr17:46660229..46663792-chr17:46665732..46668852,4	K562	blood:
3	chr17:46655425..46657433-chr17:46661001..46663692,2	MCF-7	breast:

Variant related genes	Relation type
MIR10A	TF binding region
HOXB3	TF binding region
HOXB4	TF binding region
ENSG00000120093	Chromatin interaction
ENSG00000257178	Chromatin interaction
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10853101	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2288279	0.92[JPT][hapmap]
rs2740752	0.92[JPT][hapmap]
rs3809782	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3826542	0.86[CHB][hapmap]
rs7225635	0.90[EUR][1000 genomes]
rs7405452	0.83[JPT][hapmap]
rs7406910	0.92[JPT][hapmap]
rs890431	0.92[JPT][hapmap]
rs890432	0.86[CHB][hapmap]
rs9221	0.83[JPT][hapmap]
rs9903182	0.82[JPT][hapmap]
rs9907987	0.92[JPT][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2288278	HOXB2	cis	Whole Blood	GTEx
rs2288278	HOXB-AS1	cis	Whole Blood	GTEx
rs2288278	HOXB6	cis	multi-tissue	Pritchard
rs2288278	ACLY	cis	parietal	SCAN
rs2288278	PNPO	cis	parietal	SCAN
rs2288278	KLHL11	cis	parietal	SCAN
rs2288278	NFE2L1	cis	parietal	SCAN
rs2288278	CALCOCO2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46658400-46661800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr17:46658800-46665800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr17:46659600-46662400	Weak transcription	Pancreas	Pancrea
4	chr17:46659600-46662600	Weak transcription	Gastric	stomach
5	chr17:46659800-46662200	Weak transcription	Esophagus	oesophagus
6	chr17:46660000-46661600	Enhancers	A549	lung
7	chr17:46660000-46661600	Weak transcription	HSMMtube	muscle
8	chr17:46660000-46662400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:46660000-46662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:46660000-46662600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:46660200-46661400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:46660200-46661800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:46660200-46661800	Flanking Active TSS	NHLF	lung
14	chr17:46660200-46662400	Enhancers	Primary hematopoietic stem cells	blood
15	chr17:46660200-46662400	Bivalent Enhancer	Fetal Intestine Large	intestine
16	chr17:46660400-46661400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:46660400-46661600	Weak transcription	HSMM	muscle
18	chr17:46660400-46662000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
19	chr17:46660400-46662400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:46660400-46662400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr17:46660400-46662600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr17:46660600-46661600	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr17:46660600-46661600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr17:46660600-46661600	Weak transcription	HUVEC	blood vessel
25	chr17:46660600-46661600	Enhancers	K562	blood
26	chr17:46660600-46661800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr17:46660600-46662000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:46660600-46662000	Enhancers	Adipose Nuclei	Adipose
29	chr17:46660600-46662400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr17:46660600-46662400	Enhancers	Fetal Stomach	stomach
31	chr17:46660600-46662400	Weak transcription	GM12878-XiMat	blood
32	chr17:46660800-46661600	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
33	chr17:46660800-46661600	Bivalent Enhancer	Fetal Lung	lung
34	chr17:46660800-46662000	Enhancers	Colonic Mucosa	Colon
35	chr17:46661000-46661800	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr17:46661000-46662000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:46661200-46661600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr17:46661200-46661600	Active TSS	Stomach Smooth Muscle	stomach
39	chr17:46661200-46662000	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr17:46661200-46662000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
41	chr17:46661200-46662000	Flanking Active TSS	NHDF-Ad	bronchial
42	chr17:46661200-46662400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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