Variant report

Variant	rs3826542
Chromosome Location	chr17:46629006-46629007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10853101	0.86[CHB][hapmap]
rs11652148	0.89[JPT][hapmap]
rs2229304	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288277	0.89[JPT][hapmap]
rs2288278	0.86[CHB][hapmap]
rs3809782	0.93[CHB][hapmap]
rs6504389	0.89[JPT][hapmap]
rs7225635	0.82[ASN][1000 genomes]
rs733920	0.89[JPT][hapmap]
rs7406324	0.89[JPT][hapmap]
rs7503053	0.89[JPT][hapmap]
rs890432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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
22	esv3333737	chr17:46627753-46629651	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3826542	HOXB2	cis	Whole Blood	GTEx
rs3826542	HOXB-AS1	cis	Whole Blood	GTEx
rs3826542	PYY	cis	parietal	SCAN
rs3826542	KLHL11	cis	parietal	SCAN
rs3826542	ACLY	cis	parietal	SCAN
rs3826542	PNPO	cis	parietal	SCAN
rs3826542	NAGLU	cis	parietal	SCAN
rs3826542	NFE2L1	cis	parietal	SCAN
rs3826542	KLHL11	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46621200-46629600	Weak transcription	Gastric	stomach
2	chr17:46621600-46634400	Weak transcription	Hela-S3	cervix
3	chr17:46623800-46630800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:46624000-46629800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr17:46624600-46631600	Weak transcription	Esophagus	oesophagus
6	chr17:46625600-46629600	Weak transcription	GM12878-XiMat	blood
7	chr17:46625600-46630200	Genic enhancers	Fetal Stomach	stomach
8	chr17:46625600-46631600	Weak transcription	Right Atrium	heart
9	chr17:46626200-46631600	Weak transcription	Aorta	Aorta
10	chr17:46626200-46631800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:46626400-46632200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:46626400-46632600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr17:46626400-46633200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr17:46626600-46632400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr17:46626800-46629600	Strong transcription	Adipose Nuclei	Adipose
16	chr17:46626800-46630200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr17:46626800-46632600	Transcr. at gene 5' and 3'	NHLF	lung
18	chr17:46627000-46630200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:46627200-46629800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:46627200-46632200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:46627400-46629600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr17:46627400-46630200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:46627400-46630600	Strong transcription	HUVEC	blood vessel
24	chr17:46627400-46637600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:46627600-46629400	Genic enhancers	Rectal Smooth Muscle	rectum
26	chr17:46627600-46629800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:46627600-46629800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr17:46627600-46630000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr17:46627800-46629400	Strong transcription	Colonic Mucosa	Colon
30	chr17:46627800-46629400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr17:46627800-46629600	Weak transcription	Fetal Kidney	kidney
32	chr17:46627800-46629800	Strong transcription	A549	lung
33	chr17:46627800-46630200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr17:46627800-46630200	Weak transcription	K562	blood
35	chr17:46627800-46630600	Weak transcription	HSMM	muscle
36	chr17:46628000-46630200	Weak transcription	NHDF-Ad	bronchial
37	chr17:46628200-46629400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:46628200-46629400	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr17:46628200-46629600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:46628200-46629600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:46628200-46630200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr17:46628200-46630400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:46628200-46631200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr17:46628200-46631400	Weak transcription	HSMMtube	muscle
45	chr17:46628400-46629400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:46628400-46629400	Weak transcription	Pancreas	Pancrea
47	chr17:46628400-46630200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:46628400-46630200	Bivalent Enhancer	NH-A	brain
49	chr17:46628400-46634600	Weak transcription	Spleen	Spleen
50	chr17:46628600-46629200	Bivalent Enhancer	Brain Germinal Matrix	brain

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