Variant report

Variant	rs17114459
Chromosome Location	chr5:152732763-152732764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:152723819..152726556-chr5:152729942..152732962,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10036163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10037511	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10045698	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10060758	0.81[ASN][1000 genomes]
rs11738200	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11739127	0.97[EUR][1000 genomes]
rs11741001	0.98[EUR][1000 genomes]
rs11742907	0.98[EUR][1000 genomes]
rs11749295	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12655112	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13354091	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17114463	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17114466	0.98[EUR][1000 genomes]
rs17114473	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58361474	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs72799249	0.98[EUR][1000 genomes]
rs72799252	0.98[EUR][1000 genomes]
rs72799253	0.98[EUR][1000 genomes]
rs72799254	0.98[EUR][1000 genomes]
rs72799261	0.98[EUR][1000 genomes]
rs72799264	0.98[EUR][1000 genomes]
rs72799267	0.95[EUR][1000 genomes]
rs7703714	0.81[AFR][1000 genomes]
rs7709157	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7727282	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1019051	chr5:152550863-153057896	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv868912	chr5:152582002-153095306	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv883052	chr5:152696107-152749009	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv883053	chr5:152696107-152806220	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17114459	NEK11	trans	brain	seeQTL
rs17114459	CCDC21	trans	cerebellum	SCAN
rs17114459	ZNF300P1	cis	cerebellum	SCAN
rs17114459	NMUR2	cis	cerebellum	SCAN
rs17114459	DCTN4	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152729800-152732800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr5:152730200-152734200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:152730800-152733200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:152732000-152732800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
5	chr5:152732000-152732800	Active TSS	Aorta	Aorta
6	chr5:152732000-152732800	Flanking Active TSS	HMEC	breast
7	chr5:152732000-152732800	Flanking Active TSS	NHEK	skin
8	chr5:152732000-152733000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:152732000-152733400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:152732200-152732800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:152732200-152732800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:152732200-152732800	Active TSS	Primary T cells fromperipheralblood	blood
13	chr5:152732200-152732800	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr5:152732200-152732800	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr5:152732200-152732800	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr5:152732200-152732800	Active TSS	Right Ventricle	heart
17	chr5:152732200-152732800	Active TSS	Osteobl	bone
18	chr5:152732200-152733000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:152732200-152733000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:152732200-152733000	Enhancers	Fetal Heart	heart
21	chr5:152732200-152733200	Flanking Active TSS	GM12878-XiMat	blood
22	chr5:152732400-152732800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
23	chr5:152732400-152732800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:152732400-152732800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:152732400-152732800	Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr5:152732400-152732800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:152732400-152732800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:152732400-152732800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr5:152732400-152732800	Enhancers	NH-A	brain
30	chr5:152732400-152733000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr5:152732400-152733000	Enhancers	Primary hematopoietic stem cells	blood
32	chr5:152732400-152733000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr5:152732400-152733000	Active TSS	Brain Anterior Caudate	brain
34	chr5:152732400-152733200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:152732600-152732800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:152732600-152732800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:152732600-152733000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr5:152732600-152733200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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