Variant report

Variant	rs4375701
Chromosome Location	chr17:45712218-45712219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPEPPS-1	chr17:45711118-45713021	NONHSAT054319

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10163469	0.86[EUR][1000 genomes]
rs10853090	0.95[EUR][1000 genomes]
rs11079784	0.93[EUR][1000 genomes]
rs11650372	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11656855	0.95[EUR][1000 genomes]
rs11870935	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11871606	0.93[EUR][1000 genomes]
rs12150231	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12603290	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12937560	0.81[EUR][1000 genomes]
rs12943464	0.91[EUR][1000 genomes]
rs2317826	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3760370	0.92[EUR][1000 genomes]
rs3809868	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4239162	0.89[EUR][1000 genomes]
rs4239163	0.89[EUR][1000 genomes]
rs4264433	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4289035	0.94[EUR][1000 genomes]
rs4399567	0.90[EUR][1000 genomes]
rs4580230	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4793842	0.87[EUR][1000 genomes]
rs4793908	0.89[EUR][1000 genomes]
rs4793913	0.88[EUR][1000 genomes]
rs4793978	0.93[EUR][1000 genomes]
rs4794001	0.95[EUR][1000 genomes]
rs4794016	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794047	0.85[ASN][1000 genomes]
rs4794048	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55633793	0.91[EUR][1000 genomes]
rs56226803	0.92[EUR][1000 genomes]
rs62074014	0.84[ASN][1000 genomes]
rs62074015	0.80[EUR][1000 genomes]
rs7207542	0.88[EUR][1000 genomes]
rs7210738	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7219303	0.92[EUR][1000 genomes]
rs7220935	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223029	0.92[EUR][1000 genomes]
rs73315878	0.90[EUR][1000 genomes]
rs8065437	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8065669	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8072100	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8075411	0.90[EUR][1000 genomes]
rs8077106	0.81[EUR][1000 genomes]
rs8078686	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8078880	0.90[EUR][1000 genomes]
rs8081717	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9905583	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9905922	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4375701	MRPL45P2	cis	Skin Sun Exposed Lower leg	GTEx
rs4375701	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs4375701	TBKBP1	cis	Artery Tibial	GTEx
rs4375701	TBKBP1	cis	Nerve Tibial	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45667400-45718200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr17:45691800-45716600	Weak transcription	Right Ventricle	heart
3	chr17:45692800-45714600	Weak transcription	Aorta	Aorta
4	chr17:45696600-45713600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:45696600-45726000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr17:45696800-45726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:45697000-45725800	Weak transcription	Brain Substantia Nigra	brain
8	chr17:45697200-45713400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:45697200-45713600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:45697200-45726000	Weak transcription	Brain Angular Gyrus	brain
11	chr17:45698000-45716000	Weak transcription	Psoas Muscle	Psoas
12	chr17:45698600-45714400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:45699400-45726000	Weak transcription	Brain Anterior Caudate	brain
14	chr17:45699400-45726200	Weak transcription	Fetal Kidney	kidney
15	chr17:45699600-45713800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr17:45699800-45712600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:45699800-45713400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr17:45699800-45717600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:45700000-45714000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:45700000-45725600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:45700000-45725800	Weak transcription	Spleen	Spleen
22	chr17:45700200-45713000	Weak transcription	Brain Germinal Matrix	brain
23	chr17:45700400-45725800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr17:45700600-45725200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr17:45701200-45713000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:45701400-45713200	Weak transcription	HUVEC	blood vessel
27	chr17:45701400-45718800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:45701400-45724800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr17:45701400-45725600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr17:45701400-45725800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr17:45701400-45725800	Weak transcription	Left Ventricle	heart
32	chr17:45701400-45726000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr17:45701600-45713400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr17:45701600-45714400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr17:45701800-45723800	Weak transcription	Lung	lung
36	chr17:45701800-45725600	Weak transcription	Thymus	Thymus
37	chr17:45702000-45712800	Weak transcription	Fetal Intestine Small	intestine
38	chr17:45702000-45725800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr17:45702000-45726200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr17:45702200-45713600	Weak transcription	Adipose Nuclei	Adipose
41	chr17:45702200-45725800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:45702400-45713400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr17:45702400-45725800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr17:45702600-45713800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:45702600-45713800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr17:45702600-45716000	Weak transcription	HepG2	liver
47	chr17:45702600-45720400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr17:45702600-45725800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr17:45702600-45725800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr17:45702600-45726000	Weak transcription	Brain Cingulate Gyrus	brain

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