Variant report

Variant	rs1424241
Chromosome Location	chr16:72078907-72078908
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	chr16:72072556..72075421-chr16:72076238..72078955,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11075919	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11641424	0.80[EUR][1000 genomes]
rs11648622	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12325171	1.00[YRI][hapmap]
rs12325593	0.95[YRI][hapmap]
rs13334681	1.00[YRI][hapmap]
rs13335854	0.89[YRI][hapmap]
rs16973640	1.00[YRI][hapmap]
rs16973723	0.95[YRI][hapmap]
rs4788460	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4788614	1.00[YRI][hapmap]
rs5467	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs55741258	0.81[ASN][1000 genomes]
rs56129242	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6499558	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7184834	0.95[YRI][hapmap]
rs7186117	0.95[YRI][hapmap]
rs7188150	0.95[YRI][hapmap]
rs7189506	0.94[YRI][hapmap]
rs7189654	0.95[YRI][hapmap]
rs7191270	1.00[YRI][hapmap]
rs7203195	0.95[YRI][hapmap]
rs72787038	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72787042	0.80[EUR][1000 genomes]
rs72787046	0.80[EUR][1000 genomes]
rs72787058	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7499467	0.80[EUR][1000 genomes]
rs8045316	0.95[YRI][hapmap]
rs8047881	1.00[YRI][hapmap]
rs8047930	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8056752	1.00[YRI][hapmap]
rs8057379	1.00[YRI][hapmap]
rs8061292	0.95[YRI][hapmap]
rs9921752	0.95[YRI][hapmap]
rs9925476	0.84[YRI][hapmap]
rs9925493	1.00[YRI][hapmap]
rs9932236	0.84[YRI][hapmap]
rs9940996	0.95[YRI][hapmap]
rs9972770	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
8	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription 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	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1424241	VPS4A	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72059600-72084600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr16:72060000-72079200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr16:72060200-72080000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:72060200-72095600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr16:72060200-72110600	Weak transcription	Esophagus	oesophagus
6	chr16:72062200-72079600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr16:72062200-72080000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr16:72062600-72079800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr16:72063800-72079800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr16:72075600-72079600	Enhancers	HepG2	liver
11	chr16:72076200-72098200	Weak transcription	Fetal Heart	heart
12	chr16:72076400-72079200	Weak transcription	Colon Smooth Muscle	Colon
13	chr16:72076600-72079000	Weak transcription	Placenta	Placenta
14	chr16:72076600-72079000	Weak transcription	HSMMtube	muscle
15	chr16:72076600-72084600	Weak transcription	Lung	lung
16	chr16:72076600-72092400	Weak transcription	Left Ventricle	heart
17	chr16:72077000-72107400	Weak transcription	Right Ventricle	heart
18	chr16:72077200-72080000	Weak transcription	Fetal Muscle Leg	muscle
19	chr16:72077400-72079800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr16:72077400-72081200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr16:72077400-72082800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr16:72077400-72084000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr16:72077400-72102400	Weak transcription	Brain Substantia Nigra	brain
24	chr16:72077400-72107400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr16:72077600-72084400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr16:72077600-72107400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr16:72077800-72079600	Weak transcription	Brain Germinal Matrix	brain
28	chr16:72078000-72079000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr16:72078000-72079600	Weak transcription	Fetal Brain Female	brain
30	chr16:72078000-72080200	Weak transcription	Thymus	Thymus
31	chr16:72078000-72080400	Weak transcription	Fetal Intestine Small	intestine
32	chr16:72078000-72080800	Weak transcription	Ovary	ovary
33	chr16:72078000-72083600	Weak transcription	Primary B cells from cord blood	blood
34	chr16:72078000-72084400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr16:72078000-72090000	Weak transcription	Gastric	stomach
36	chr16:72078000-72100800	Weak transcription	Brain Hippocampus Middle	brain
37	chr16:72078000-72103200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr16:72078200-72079000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr16:72078200-72080200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr16:72078200-72095600	Weak transcription	Brain Anterior Caudate	brain
41	chr16:72078200-72105200	Weak transcription	Brain Angular Gyrus	brain
42	chr16:72078400-72081600	Weak transcription	Fetal Stomach	stomach
43	chr16:72078400-72084600	Weak transcription	Adipose Nuclei	Adipose
44	chr16:72078400-72098400	Weak transcription	Primary T cells from cord blood	blood
45	chr16:72078400-72105400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr16:72078400-72108000	Weak transcription	Aorta	Aorta
47	chr16:72078600-72080000	Enhancers	Liver	Liver
48	chr16:72078600-72083200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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