Variant report

Variant	rs4497739
Chromosome Location	chr17:45616332-45616333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45608528..45610827-chr17:45614421..45616919,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141279	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11079774	0.88[CEU][hapmap]
rs11079783	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11079784	0.80[CEU][hapmap]
rs11651643	0.84[CEU][hapmap]
rs11870585	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12452796	0.84[CEU][hapmap]
rs1912482	0.85[CEU][hapmap]
rs1912483	0.85[CEU][hapmap]
rs1912484	0.89[CEU][hapmap];0.87[JPT][hapmap]
rs1912486	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs1912487	0.86[CEU][hapmap]
rs1962307	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2013383	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs2175290	0.80[CEU][hapmap]
rs2611998	0.86[AMR][1000 genomes]
rs3736438	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs3760371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3826536	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs3851808	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4267364	0.81[JPT][hapmap]
rs4794047	0.85[CEU][hapmap]
rs4794052	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs4794053	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs4968257	0.89[CEU][hapmap];0.87[JPT][hapmap]
rs4968318	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4968319	0.85[CEU][hapmap]
rs6503796	0.84[CEU][hapmap]
rs6503804	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs6503807	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs7214410	0.81[CEU][hapmap]
rs7214799	0.92[CEU][hapmap];0.94[YRI][hapmap]
rs7222225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8075058	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs8075566	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs8075843	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs8078309	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs8079142	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9889709	0.89[CEU][hapmap]
rs9905581	0.92[CEU][hapmap]
rs9912311	0.86[CEU][hapmap]
rs9913503	0.84[CEU][hapmap]
rs9915919	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:37 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv516872	chr17:45419139-45702280	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv525267	chr17:45451894-45735706	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1806110	chr17:45477544-45673592	Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv833468	chr17:45511563-45683164	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv469573	chr17:45511582-45698942	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv471701	chr17:45511583-45698942	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1793478	chr17:45518444-45671051	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	esv1808961	chr17:45542951-45664746	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
15	esv33689	chr17:45551959-45664575	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	nsv471513	chr17:45552080-45671439	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv908570	chr17:45571502-45684651	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	esv1818529	chr17:45583088-45683095	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	nsv962334	chr17:45600707-45632564	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv471403	chr17:45608444-45700642	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
21	nsv482203	chr17:45608444-45700642	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
22	esv1811254	chr17:45609466-45673592	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	esv1808701	chr17:45610793-45675401	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv821341	chr17:45611031-45671632	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	nsv828033	chr17:45611031-45671632	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	esv1814312	chr17:45611212-45683095	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	nsv9568	chr17:45613661-45672773	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
28	esv1803315	chr17:45616076-45618848	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	esv1816359	chr17:45616076-45619418	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	esv1800121	chr17:45616076-45620335	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	esv1821396	chr17:45616076-45620335	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	esv1817118	chr17:45616076-45622938	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	esv1849392	chr17:45616076-45633336	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
34	esv1849810	chr17:45616076-45633336	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
35	esv10606	chr17:45616210-45620061	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
36	esv12768	chr17:45616210-45671173	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
37	nsv514851	chr17:45616237-45663269	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4497739	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4497739	TBKBP1	cis	Artery Tibial	GTEx
rs4497739	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs4497739	TBKBP1	cis	Nerve Tibial	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45609800-45624800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:45610000-45617400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:45610000-45623400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:45610000-45624000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:45610000-45624400	Weak transcription	Placenta	Placenta
6	chr17:45610000-45624800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:45610000-45630000	Weak transcription	Gastric	stomach
8	chr17:45610000-45638600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr17:45610000-45639000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr17:45610000-45670600	Weak transcription	Lung	lung
11	chr17:45610000-45670600	Weak transcription	Pancreas	Pancrea
12	chr17:45610000-45676800	Weak transcription	Ovary	ovary
13	chr17:45610200-45674200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr17:45610400-45617800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:45610400-45617800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr17:45610400-45623400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr17:45610400-45624600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:45610400-45633800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr17:45610400-45637600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr17:45610400-45637800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr17:45610400-45639200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr17:45610400-45646800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr17:45610400-45647000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr17:45610400-45647600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr17:45610400-45647600	Weak transcription	Osteobl	bone
26	chr17:45610400-45662600	Weak transcription	Adipose Nuclei	Adipose
27	chr17:45610400-45670600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:45610600-45617400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:45610600-45617800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr17:45610600-45623400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr17:45610600-45623400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:45610600-45623400	Weak transcription	Fetal Intestine Large	intestine
33	chr17:45610600-45624000	Weak transcription	Fetal Stomach	stomach
34	chr17:45610600-45624000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr17:45610600-45624600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:45610600-45626400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:45610600-45626400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr17:45610600-45637200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr17:45610600-45647000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr17:45610600-45647000	Weak transcription	Dnd41	blood
41	chr17:45610600-45662200	Weak transcription	HSMM	muscle
42	chr17:45610600-45669200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr17:45610600-45670200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr17:45610800-45623400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr17:45610800-45624600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr17:45610800-45669000	Weak transcription	NH-A	brain
47	chr17:45611000-45618400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr17:45611000-45623600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr17:45611000-45647000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:45611200-45616400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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