Variant report

Variant	rs3826536
Chromosome Location	chr17:45501967-45501968
allele	A/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	chr17:45501526-45502268	GM12891	blood:	n/a	n/a
2	POLR2A	chr17:45501845-45502133	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr17:45501842-45502059	GM12891	blood:	n/a	n/a
4	POLR2A	chr17:45501774-45502157	GM12892	blood:	n/a	n/a
5	POLR2A	chr17:45501720-45502190	GM12892	blood:	n/a	n/a
6	POLR2A	chr17:45501915-45502042	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:45501854-45502234	GM12891	blood:	n/a	n/a
8	POLR2A	chr17:45501346-45502330	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr17:45501719-45502285	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:45501847-45502075	GM12878	blood:	n/a	n/a
11	POLR2A	chr17:45501753-45502263	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000253347	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11079774	0.85[CEU][hapmap]
rs11079776	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11079783	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs11651643	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11651766	0.81[ASN][1000 genomes]
rs12948299	0.88[CEU][hapmap];0.82[YRI][hapmap]
rs1912484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1912485	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1912486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2136749	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2136750	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2292346	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3736438	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3760371	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs3851808	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	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4114873	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4497739	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs4968228	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968259	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57427906	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7214993	0.95[JPT][hapmap]
rs7216112	0.88[CEU][hapmap]
rs7221224	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7222225	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs8074451	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8075058	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8075843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8079142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9807106	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9894594	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9895509	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9895776	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9899859	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9900123	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9903100	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9904967	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9905073	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9905581	0.82[CEU][hapmap]
rs9908049	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9913014	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9913206	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9915222	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
5	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
6	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
7	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
8	esv1801088	chr17:45435575-45522311	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1056191	chr17:45442007-45519072	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	esv3419507	chr17:45500407-45506076	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv960118	chr17:45501749-45503835	Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3826536	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs3826536	TBKBP1	cis	Artery Tibial	GTEx
rs3826536	TBKBP1	cis	Nerve Tibial	GTEx
rs3826536	TBKBP1	cis	lung	GTEx
rs3826536	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45490800-45502400	Weak transcription	HepG2	liver
2	chr17:45500400-45502000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr17:45500400-45502000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr17:45500600-45502000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr17:45500600-45502000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr17:45500600-45502000	Active TSS	Fetal Intestine Large	intestine
7	chr17:45500600-45502000	Active TSS	Fetal Intestine Small	intestine
8	chr17:45500600-45502000	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr17:45500600-45502200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr17:45500600-45511200	Weak transcription	K562	blood
11	chr17:45500800-45502000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr17:45500800-45502000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr17:45500800-45506800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr17:45501000-45502000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:45501400-45502600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr17:45501400-45504800	Weak transcription	A549	lung
17	chr17:45501400-45514600	Weak transcription	Primary T cells from cord blood	blood
18	chr17:45501400-45554200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:45501400-45554400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr17:45501600-45502000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:45501600-45503400	Weak transcription	NHLF	lung
22	chr17:45501600-45505600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:45501600-45509800	Weak transcription	Pancreas	Pancrea
24	chr17:45501600-45511400	Weak transcription	Esophagus	oesophagus
25	chr17:45501600-45511800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:45501600-45511800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:45501600-45515600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:45501600-45520200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:45501600-45555400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:45501600-45556400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr17:45501800-45502600	Weak transcription	Dnd41	blood
32	chr17:45501800-45502800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr17:45501800-45503400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr17:45501800-45504600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr17:45501800-45504800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr17:45501800-45505600	Weak transcription	Liver	Liver
37	chr17:45501800-45507800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr17:45501800-45508800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr17:45501800-45511800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr17:45501800-45511800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:45501800-45512400	Weak transcription	Primary B cells from cord blood	blood
42	chr17:45501800-45533400	Weak transcription	Gastric	stomach
43	chr17:45501800-45547400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr17:45501800-45550200	Weak transcription	Ovary	ovary

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