Variant report

Variant	rs1445708
Chromosome Location	chr5:115298977-115298978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10065502	1.00[JPT][hapmap]
rs10463449	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs10463451	0.88[CEU][hapmap];0.87[MKK][hapmap];0.87[EUR][1000 genomes]
rs10463452	0.80[JPT][hapmap]
rs10463675	0.92[CEU][hapmap];0.85[GIH][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs10519436	1.00[JPT][hapmap]
rs10519437	1.00[JPT][hapmap]
rs10900709	1.00[JPT][hapmap]
rs1117291	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11241343	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs11241345	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs11241347	0.80[JPT][hapmap]
rs12186351	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1346479	1.00[JPT][hapmap]
rs1428086	1.00[JPT][hapmap]
rs1445706	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17138510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs34392129	0.87[EUR][1000 genomes]
rs34463406	0.86[EUR][1000 genomes]
rs4921040	1.00[JPT][hapmap]
rs4921045	1.00[JPT][hapmap]
rs4921047	1.00[JPT][hapmap]
rs4921050	1.00[JPT][hapmap]
rs6594920	0.85[EUR][1000 genomes]
rs6594921	0.88[CEU][hapmap];0.82[GIH][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs7704078	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7713570	0.84[CEU][hapmap];0.82[GIH][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv515611	chr5:115208843-115428381	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1021968	chr5:115213162-115426468	Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1024008	chr5:115222974-115431050	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1027117	chr5:115222974-115442883	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763487	chr5:115222986-115442895	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv462400	chr5:115223504-115428381	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription 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	23 gene(s)	inside rSNPs	diseases
9	nsv599478	chr5:115223504-115428381	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv1030480	chr5:115228889-115446861	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv599479	chr5:115233116-115450969	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv1029427	chr5:115236239-115387283	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	nsv1015976	chr5:115236239-115434163	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv537868	chr5:115236239-115434163	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
15	nsv882735	chr5:115254723-115377150	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv882736	chr5:115254723-115552945	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	nsv882737	chr5:115263853-115552945	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1445708	NPVF	trans	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115296800-115299000	Bivalent Enhancer	Fetal Brain Male	brain
2	chr5:115296800-115299000	Enhancers	Spleen	Spleen
3	chr5:115296800-115299000	Flanking Bivalent TSS/Enh	Osteobl	bone
4	chr5:115296800-115299200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr5:115296800-115299800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr5:115297000-115299000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:115297000-115299000	Bivalent/Poised TSS	HSMM	muscle
8	chr5:115297000-115299200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr5:115297000-115299800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr5:115297200-115299000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr5:115297200-115299000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
12	chr5:115297200-115299000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
13	chr5:115297200-115299000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
14	chr5:115297200-115299000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:115297200-115299000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:115297200-115299000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:115297200-115299200	Active TSS	Right Atrium	heart
18	chr5:115297200-115299400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr5:115297400-115299000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:115297400-115299000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:115297400-115299200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr5:115297600-115299000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:115297600-115299000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:115297600-115299000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:115297800-115299000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:115297800-115299000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:115297800-115299000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr5:115297800-115299200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr5:115298000-115299000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:115298000-115299000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:115298000-115299000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:115298000-115299000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
33	chr5:115298000-115299000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:115298000-115299000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr5:115298000-115299000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr5:115298000-115299000	Bivalent Enhancer	Fetal Heart	heart
37	chr5:115298000-115299000	Bivalent Enhancer	Stomach Mucosa	stomach
38	chr5:115298000-115299200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
39	chr5:115298000-115299600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
40	chr5:115298000-115300200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:115298200-115299000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
42	chr5:115298200-115299000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
43	chr5:115298200-115299000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
44	chr5:115298200-115299000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:115298200-115299000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:115298200-115299000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
47	chr5:115298200-115299000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
48	chr5:115298200-115299000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
49	chr5:115298200-115299000	Flanking Bivalent TSS/Enh	Left Ventricle	heart
50	chr5:115298200-115299000	Flanking Active TSS	Pancreas	Pancrea

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