Variant report

Variant	rs4968257
Chromosome Location	chr17:45430534-45430535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11079774	0.85[CEU][hapmap]
rs11079776	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11651643	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11651766	0.81[ASN][1000 genomes]
rs1221385	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12948299	0.88[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1912484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912485	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1912486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2136749	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136750	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292346	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736438	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3826536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3851808	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]
rs3871595	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4114873	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4497739	0.89[CEU][hapmap];0.87[JPT][hapmap]
rs4968228	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968259	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57427906	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7214993	0.95[JPT][hapmap]
rs7216112	0.88[CEU][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs7221224	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8074451	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8075058	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8075843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807106	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894594	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9895509	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9895776	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9899859	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9900123	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9903100	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9904967	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9905073	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9905581	0.82[CEU][hapmap]
rs9908049	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9913014	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9913206	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9915222	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4968257	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4968257	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs4968257	TBKBP1	cis	Artery Tibial	GTEx
rs4968257	TBKBP1	cis	Nerve Tibial	GTEx
rs4968257	TBKBP1	cis	lung	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45402000-45442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:45402200-45446400	Weak transcription	Colon Smooth Muscle	Colon
3	chr17:45402200-45500800	Weak transcription	Aorta	Aorta
4	chr17:45402400-45433600	Weak transcription	Fetal Heart	heart
5	chr17:45402400-45433600	Weak transcription	Fetal Intestine Small	intestine
6	chr17:45402400-45433600	Weak transcription	Fetal Stomach	stomach
7	chr17:45402400-45435800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr17:45402400-45436000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr17:45402800-45440800	Weak transcription	Primary T cells from cord blood	blood
10	chr17:45407600-45435800	Weak transcription	Fetal Intestine Large	intestine
11	chr17:45411600-45468200	Weak transcription	Left Ventricle	heart
12	chr17:45412400-45463400	Weak transcription	Gastric	stomach
13	chr17:45413400-45463800	Weak transcription	Ovary	ovary
14	chr17:45421800-45449800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr17:45422000-45433200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr17:45423000-45435000	Weak transcription	Liver	Liver
17	chr17:45423000-45450000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr17:45423000-45465400	Weak transcription	Adipose Nuclei	Adipose
19	chr17:45423200-45435000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr17:45423200-45450000	Weak transcription	Primary B cells from cord blood	blood
21	chr17:45423400-45431400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:45425000-45432000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:45425000-45438600	Weak transcription	Primary B cells from peripheral blood	blood

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