Variant report

Variant	rs4439799
Chromosome Location	chr17:45781599-45781600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45776981..45779433-chr17:45781232..45782941,2	MCF-7	breast:
2	chr17:45780593..45782883-chr17:45859377..45861716,2	K562	blood:
3	chr17:45777137..45782464-chr17:45784675..45788885,8	K562	blood:
4	chr17:45781571..45784381-chr17:48942230..48945261,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229980	Chromatin interaction
ENSG00000141232	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11870935	0.81[CEU][hapmap];0.81[CHD][hapmap]
rs12943464	0.80[CEU][hapmap]
rs2317826	0.85[CEU][hapmap]
rs3809868	0.85[CEU][hapmap];0.81[CHD][hapmap]
rs4561509	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794048	0.85[CEU][hapmap];0.81[CHD][hapmap]
rs4794057	0.86[EUR][1000 genomes]
rs62074055	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67919208	0.91[EUR][1000 genomes]
rs7210738	0.85[CEU][hapmap];0.81[CHD][hapmap]
rs8065669	0.85[CEU][hapmap];0.81[CHD][hapmap]
rs8070463	0.92[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs8072100	0.84[CEU][hapmap]
rs8078686	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv908571	chr17:45765249-45821510	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs4439799	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4439799	TBKBP1	cis	Thyroid	GTEx
rs4439799	TBKBP1	cis	Nerve Tibial	GTEx
rs4439799	NPEPPS	cis	parietal	SCAN
rs4439799	TBKBP1	cis	lung	GTEx
rs4439799	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs4439799	C17orf57	cis	parietal	SCAN
rs4439799	CDK5RAP3	cis	cerebellum	SCAN
rs4439799	DBF4B	cis	cerebellum	SCAN
rs4439799	TBKBP1	cis	Artery Aorta	GTEx
rs4439799	TBKBP1	cis	Whole Blood	GTEx
rs4439799	C17orf65	cis	cerebellum	SCAN
rs4439799	VPS25	cis	parietal	SCAN
rs4439799	RAB5C	cis	parietal	SCAN
rs4439799	VPS25	cis	cerebellum	SCAN
rs4439799	TBKBP1	cis	lymphoblastoid	seeQTL
rs4439799	TBKBP1	cis	Artery Tibial	GTEx
rs4439799	SLC25A39	cis	parietal	SCAN
rs4439799	C17orf57	cis	cerebellum	SCAN
rs4439799	MRPL45P2	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45772600-45783600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:45772800-45783800	Weak transcription	HSMMtube	muscle
3	chr17:45772800-45783800	Weak transcription	NHDF-Ad	bronchial
4	chr17:45773000-45782000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr17:45773000-45783800	Weak transcription	Brain Angular Gyrus	brain
6	chr17:45773200-45782200	Weak transcription	Brain Substantia Nigra	brain
7	chr17:45773200-45783600	Weak transcription	Brain Anterior Caudate	brain
8	chr17:45773200-45783600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr17:45773400-45781800	Weak transcription	Psoas Muscle	Psoas
10	chr17:45773400-45783800	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:45773400-45783800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr17:45773400-45784800	Weak transcription	Osteobl	bone
13	chr17:45773400-45785600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:45773400-45790600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr17:45773600-45783800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:45774000-45781800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:45774000-45781800	Weak transcription	Right Atrium	heart
18	chr17:45774000-45783400	Strong transcription	Fetal Intestine Small	intestine
19	chr17:45774200-45783600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr17:45774600-45783200	Weak transcription	Fetal Kidney	kidney
21	chr17:45775000-45782600	Strong transcription	Lung	lung
22	chr17:45775000-45785200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr17:45775000-45790800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr17:45776400-45782200	Weak transcription	HepG2	liver
25	chr17:45776600-45783800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr17:45776600-45785600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr17:45776800-45781600	Strong transcription	Fetal Brain Female	brain
28	chr17:45777000-45781600	Weak transcription	Pancreas	Pancrea
29	chr17:45777000-45781800	Weak transcription	Left Ventricle	heart
30	chr17:45777200-45781800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr17:45777200-45783800	Weak transcription	NHLF	lung
32	chr17:45778000-45782800	Weak transcription	Esophagus	oesophagus
33	chr17:45778200-45783400	Weak transcription	Fetal Lung	lung
34	chr17:45778200-45785600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr17:45778400-45781600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr17:45778600-45783600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr17:45778600-45784400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr17:45778600-45784400	Weak transcription	Fetal Intestine Large	intestine
39	chr17:45778600-45786000	Weak transcription	Aorta	Aorta
40	chr17:45778600-45788200	Weak transcription	HUVEC	blood vessel
41	chr17:45778800-45782000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr17:45778800-45782400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:45778800-45783800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:45778800-45784200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr17:45778800-45785000	Enhancers	Primary B cells from cord blood	blood
46	chr17:45779000-45783600	Genic enhancers	Fetal Muscle Trunk	muscle
47	chr17:45779000-45785400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr17:45779200-45782400	Weak transcription	Gastric	stomach
49	chr17:45779200-45785200	Enhancers	Primary hematopoietic stem cells	blood
50	chr17:45779200-45785400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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