Variant report

Variant	rs9900123
Chromosome Location	chr17:45549055-45549056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11079776	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650210	0.86[ASN][1000 genomes]
rs11651643	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11651766	0.90[ASN][1000 genomes]
rs1221385	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12449647	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12451409	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12944103	0.84[AFR][1000 genomes]
rs1912484	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1912485	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1912486	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2136749	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2136750	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292346	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28458768	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28507314	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs3736438	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3826536	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3851808	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3871595	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4114873	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4968228	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968257	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968259	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968318	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57427906	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62076541	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7208530	0.85[AFR][1000 genomes]
rs7221224	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8074451	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8075058	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8075843	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8079142	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9807106	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9892497	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9894594	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9895509	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895776	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9897063	0.85[ASN][1000 genomes]
rs9899859	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9901869	0.85[ASN][1000 genomes]
rs9903100	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9904967	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9905073	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9905581	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9907159	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9908016	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9908049	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9912101	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9913014	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9913206	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9915222	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv908566	chr17:45465735-45569714	Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv908568	chr17:45506682-45590420	Enhancers Weak transcription Strong transcription 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	4 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv908569	chr17:45537395-45603094	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9900123	TBKBP1	cis	Artery Tibial	GTEx
rs9900123	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs9900123	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs9900123	TBKBP1	cis	Nerve Tibial	GTEx
rs9900123	TBKBP1	cis	lung	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45501400-45554200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:45501400-45554400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr17:45501600-45555400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr17:45501600-45556400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr17:45501800-45550200	Weak transcription	Ovary	ovary
6	chr17:45505200-45550200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:45507200-45555000	Weak transcription	Fetal Thymus	thymus
8	chr17:45507600-45554200	Weak transcription	Left Ventricle	heart
9	chr17:45512200-45550200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:45515400-45551600	Weak transcription	Fetal Intestine Large	intestine
11	chr17:45515600-45554200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:45516000-45556400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr17:45516800-45553200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr17:45517000-45550600	Weak transcription	Adipose Nuclei	Adipose
15	chr17:45517600-45550200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:45518000-45568800	Weak transcription	K562	blood
17	chr17:45518200-45554200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr17:45518400-45550200	Weak transcription	Lung	lung
19	chr17:45518600-45569200	Weak transcription	Brain Anterior Caudate	brain
20	chr17:45519000-45551600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr17:45519400-45569400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr17:45519600-45550200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr17:45519800-45555000	Weak transcription	Thymus	Thymus
24	chr17:45520000-45550600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr17:45520200-45549200	Weak transcription	HepG2	liver
26	chr17:45521000-45550800	Weak transcription	Osteobl	bone
27	chr17:45523200-45556400	Weak transcription	GM12878-XiMat	blood
28	chr17:45526200-45556000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr17:45526400-45568800	Weak transcription	Brain Angular Gyrus	brain
30	chr17:45526600-45568800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr17:45527000-45568800	Weak transcription	Colon Smooth Muscle	Colon
32	chr17:45527800-45568800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr17:45528200-45550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:45528800-45550400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:45529000-45549400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:45529800-45558200	Weak transcription	Brain Hippocampus Middle	brain
37	chr17:45530200-45568800	Weak transcription	A549	lung
38	chr17:45530400-45554400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr17:45530600-45550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr17:45531000-45550800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr17:45531200-45560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr17:45531400-45568800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr17:45531600-45555000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr17:45531600-45569200	Weak transcription	Primary T cells from cord blood	blood
45	chr17:45534800-45569400	Weak transcription	Esophagus	oesophagus
46	chr17:45536000-45549400	Weak transcription	Dnd41	blood
47	chr17:45537800-45569000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr17:45538200-45551600	Weak transcription	Fetal Brain Female	brain
49	chr17:45538200-45569000	Weak transcription	Brain Substantia Nigra	brain
50	chr17:45539800-45569400	Weak transcription	Brain Germinal Matrix	brain

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