Variant report

Variant	rs9905308
Chromosome Location	chr17:45409386-45409387
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45399600..45403116-chr17:45404916..45409576,7	K562	blood:

Variant related genes	Relation type
ENSG00000263293	Chromatin interaction
ENSG00000178852	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11079774	0.89[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12452796	0.89[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12453233	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1912482	0.89[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1912483	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1912487	0.90[CEU][hapmap]
rs2136751	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2175290	0.85[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs35016056	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4968317	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4968319	0.89[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs56952963	0.82[AFR][1000 genomes]
rs7214410	0.85[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7220606	0.81[ASN][1000 genomes]
rs7221196	0.81[ASN][1000 genomes]
rs7221345	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889709	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9890782	0.82[AMR][1000 genomes]
rs9893901	1.00[YRI][hapmap]
rs9895746	0.82[AFR][1000 genomes]
rs9897492	0.84[AMR][1000 genomes]
rs9900360	0.82[AFR][1000 genomes]
rs9905581	0.82[CEU][hapmap]
rs9912311	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs9912450	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9915919	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9905308	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs9905308	TBKBP1	cis	Nerve Tibial	GTEx
rs9905308	MRPL45P2	cis	Muscle Skeletal	GTEx

Chromatin state (count:45 , 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	chr17:45402200-45416800	Weak transcription	Lung	lung
4	chr17:45402200-45420400	Weak transcription	Pancreas	Pancrea
5	chr17:45402200-45446400	Weak transcription	Colon Smooth Muscle	Colon
6	chr17:45402200-45500800	Weak transcription	Aorta	Aorta
7	chr17:45402400-45411000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr17:45402400-45412200	Weak transcription	Adipose Nuclei	Adipose
9	chr17:45402400-45412800	Weak transcription	Ovary	ovary
10	chr17:45402400-45416000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr17:45402400-45419400	Weak transcription	Liver	Liver
12	chr17:45402400-45419600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr17:45402400-45421200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr17:45402400-45421400	Weak transcription	Fetal Kidney	kidney
15	chr17:45402400-45421600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr17:45402400-45423400	Weak transcription	NHDF-Ad	bronchial
17	chr17:45402400-45424200	Weak transcription	Fetal Brain Male	brain
18	chr17:45402400-45427200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr17:45402400-45428400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr17:45402400-45433600	Weak transcription	Fetal Heart	heart
21	chr17:45402400-45433600	Weak transcription	Fetal Intestine Small	intestine
22	chr17:45402400-45433600	Weak transcription	Fetal Stomach	stomach
23	chr17:45402400-45435800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr17:45402400-45436000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:45402600-45416800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:45402600-45422200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:45402600-45423000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr17:45402600-45423400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr17:45402600-45424600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr17:45402600-45428800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr17:45402800-45422400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr17:45402800-45440800	Weak transcription	Primary T cells from cord blood	blood
33	chr17:45403000-45413000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr17:45403000-45429400	Weak transcription	Placenta	Placenta
35	chr17:45407600-45435800	Weak transcription	Fetal Intestine Large	intestine
36	chr17:45408200-45421000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr17:45408400-45409800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr17:45408800-45409400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:45408800-45410200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:45408800-45411000	Strong transcription	Primary B cells from cord blood	blood
41	chr17:45408800-45411200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:45409000-45409600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:45409200-45410400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr17:45409200-45413600	Weak transcription	Fetal Muscle Leg	muscle
45	chr17:45409200-45425200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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