Variant report

Variant	rs3851808
Chromosome Location	chr17:45425144-45425145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11079776	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11651643	1.00[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1221385	0.83[EUR][1000 genomes]
rs12948299	1.00[ASW][hapmap];0.83[LWK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1912484	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1912485	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1912486	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2136749	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2136750	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292346	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736438	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3826536	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3871595	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4114873	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4497739	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4968228	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4968257	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968259	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968318	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57427906	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7214993	0.90[JPT][hapmap]
rs7216112	0.81[LWK][hapmap];0.84[MEX][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs7221224	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8074451	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8075058	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8075843	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8079142	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9807106	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9894594	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9895509	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9895776	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9899859	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9900123	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9903100	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9904967	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9905073	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9908049	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9913014	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9913206	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9915222	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv962445	chr17:45397004-45428018	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1062096	chr17:45416538-45518683	Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv470590	chr17:45419138-45547077	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1818362	chr17:45419139-45499396	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv457821	chr17:45419139-45547078	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv575462	chr17:45419139-45547078	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	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
9	nsv908564	chr17:45422628-45522311	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3851808	TBKBP1	cis	Artery Tibial	GTEx
rs3851808	NFE2L1	cis	parietal	SCAN
rs3851808	KRTAP9-3	cis	cerebellum	SCAN
rs3851808	TBKBP1	cis	Nerve Tibial	GTEx
rs3851808	TBKBP1	cis	lung	GTEx
rs3851808	MRPL45P2	cis	lymphoblastoid	seeQTL
rs3851808	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs3851808	TBKBP1	cis	lymphoblastoid	seeQTL
rs3851808	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs3851808	HOXB2	cis	cerebellum	SCAN
rs3851808	VPS25	cis	cerebellum	SCAN
rs3851808	C17orf57	cis	parietal	SCAN
rs3851808	C17orf57	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45402000-45428600	Weak transcription	Spleen	Spleen
2	chr17:45402000-45442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:45402200-45446400	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:45402200-45500800	Weak transcription	Aorta	Aorta
5	chr17:45402400-45427200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr17:45402400-45428400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr17:45402400-45433600	Weak transcription	Fetal Heart	heart
8	chr17:45402400-45433600	Weak transcription	Fetal Intestine Small	intestine
9	chr17:45402400-45433600	Weak transcription	Fetal Stomach	stomach
10	chr17:45402400-45435800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr17:45402400-45436000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr17:45402600-45428800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr17:45402800-45440800	Weak transcription	Primary T cells from cord blood	blood
14	chr17:45403000-45429400	Weak transcription	Placenta	Placenta
15	chr17:45407600-45435800	Weak transcription	Fetal Intestine Large	intestine
16	chr17:45409200-45425200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:45411600-45468200	Weak transcription	Left Ventricle	heart
18	chr17:45412400-45463400	Weak transcription	Gastric	stomach
19	chr17:45413400-45463800	Weak transcription	Ovary	ovary
20	chr17:45421800-45449800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr17:45422000-45433200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr17:45423000-45426000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:45423000-45435000	Weak transcription	Liver	Liver
24	chr17:45423000-45450000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr17:45423000-45465400	Weak transcription	Adipose Nuclei	Adipose
26	chr17:45423200-45426600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:45423200-45435000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr17:45423200-45450000	Weak transcription	Primary B cells from cord blood	blood
29	chr17:45423400-45431400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:45424800-45428000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr17:45425000-45432000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:45425000-45438600	Weak transcription	Primary B cells from peripheral blood	blood

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