Variant report

Variant	rs4092460
Chromosome Location	chr17:45667550-45667551
allele	C/T
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	chr17:45667418-45667558	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
NPEPPS	TF binding region

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10163469	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10432035	0.81[ASN][1000 genomes]
rs10853090	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11079779	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11079782	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079784	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1138193	0.91[ASN][1000 genomes]
rs11650372	0.81[EUR][1000 genomes]
rs11656855	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11871606	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12150231	0.81[EUR][1000 genomes]
rs12603290	0.83[EUR][1000 genomes]
rs12936468	0.94[ASN][1000 genomes]
rs12937560	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12943464	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2125873	0.85[ASN][1000 genomes]
rs35919601	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3760370	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3865314	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4239162	0.86[ASN][1000 genomes]
rs4239163	0.86[ASN][1000 genomes]
rs4289035	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4399567	0.88[ASN][1000 genomes]
rs4793836	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4793842	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793908	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793913	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793978	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794001	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794016	0.80[EUR][1000 genomes]
rs55633793	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56226803	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62074014	0.88[EUR][1000 genomes]
rs62074015	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505049	0.93[ASN][1000 genomes]
rs7207542	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7210472	0.82[EUR][1000 genomes]
rs7213086	0.88[ASN][1000 genomes]
rs7214799	0.90[ASN][1000 genomes]
rs7219303	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7220935	0.83[EUR][1000 genomes]
rs7223029	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73315878	0.86[ASN][1000 genomes]
rs8065437	0.81[EUR][1000 genomes]
rs8065669	0.80[EUR][1000 genomes]
rs8070759	0.82[EUR][1000 genomes]
rs8072100	0.86[EUR][1000 genomes]
rs8072644	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8075411	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8078880	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8082284	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9635762	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9635763	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9891111	0.90[ASN][1000 genomes]
rs9905922	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:44 , 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	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	esv1807916	chr17:45616653-45668909	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	esv1815163	chr17:45616653-45675272	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
28	esv1809431	chr17:45619018-45670038	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
29	esv1810470	chr17:45619935-45670038	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	diseases
30	esv1805152	chr17:45630082-45670038	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	diseases
31	esv995713	chr17:45632210-45673517	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases
32	esv1843304	chr17:45634173-45670038	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	diseases
33	esv1851806	chr17:45634173-45670038	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases
34	esv1851394	chr17:45634373-45668909	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	diseases
35	esv1851549	chr17:45634373-45668909	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	diseases
36	esv1851900	chr17:45634373-45673592	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	diseases
37	esv1851117	chr17:45635179-45671051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
38	esv1847040	chr17:45635179-45683095	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
39	nsv962335	chr17:45645901-45669882	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
40	esv1799225	chr17:45650581-45670822	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
41	esv3401092	chr17:45662853-45667951	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
42	esv3326159	chr17:45664203-45671351	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
43	esv3437736	chr17:45666753-45671451	Strong transcription Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
44	esv3346004	chr17:45666853-45671151	Weak transcription Strong transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4092460	TBKBP1	cis	Artery Tibial	GTEx
rs4092460	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs4092460	TBKBP1	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45610000-45670600	Weak transcription	Lung	lung
2	chr17:45610000-45670600	Weak transcription	Pancreas	Pancrea
3	chr17:45610000-45676800	Weak transcription	Ovary	ovary
4	chr17:45610200-45674200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr17:45610400-45670600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr17:45610600-45669200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:45610600-45670200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr17:45610800-45669000	Weak transcription	NH-A	brain
9	chr17:45611200-45674800	Weak transcription	Primary B cells from cord blood	blood
10	chr17:45616600-45674600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:45618600-45674600	Weak transcription	Fetal Brain Female	brain
12	chr17:45618800-45669200	Weak transcription	HUVEC	blood vessel
13	chr17:45619400-45668200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr17:45622800-45669000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr17:45623600-45671000	Weak transcription	Esophagus	oesophagus
16	chr17:45625000-45668200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr17:45625200-45670600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:45629800-45673400	Weak transcription	K562	blood
19	chr17:45635400-45670600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr17:45637400-45669000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr17:45637400-45670600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr17:45637800-45678800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr17:45638800-45669200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr17:45639600-45675000	Weak transcription	Brain Angular Gyrus	brain
25	chr17:45639800-45676800	Weak transcription	Brain Anterior Caudate	brain
26	chr17:45641000-45678000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr17:45641400-45675000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr17:45644200-45675200	Weak transcription	GM12878-XiMat	blood
29	chr17:45644400-45683800	Weak transcription	Spleen	Spleen
30	chr17:45644600-45673400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:45644600-45673600	Weak transcription	Hela-S3	cervix
32	chr17:45645000-45673800	Weak transcription	HMEC	breast
33	chr17:45645600-45678200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:45647800-45669200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:45647800-45677000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr17:45647800-45684800	Weak transcription	Gastric	stomach
37	chr17:45648000-45670600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr17:45648000-45670600	Weak transcription	Osteobl	bone
39	chr17:45648200-45667800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr17:45649600-45670200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:45649600-45675200	Weak transcription	Right Ventricle	heart
42	chr17:45650000-45673200	Weak transcription	HepG2	liver
43	chr17:45654800-45672800	Weak transcription	NHDF-Ad	bronchial
44	chr17:45657200-45688200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:45657400-45670600	Weak transcription	Colonic Mucosa	Colon
46	chr17:45657800-45678800	Weak transcription	NHEK	skin
47	chr17:45659000-45676800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr17:45659200-45678600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr17:45659200-45698800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:45659600-45675000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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