Variant report

Variant	rs17080199
Chromosome Location	chr5:179766927-179766928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1078646	0.87[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs1559114	0.88[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs17080196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4235511	0.81[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs4566752	0.88[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs4700736	0.81[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs4700943	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62404950	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62404953	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62404956	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62404958	0.93[ASN][1000 genomes]
rs62404959	0.94[ASN][1000 genomes]
rs62406364	0.89[ASN][1000 genomes]
rs6601110	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs6859159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6864729	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6870028	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6871454	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6874176	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6884111	1.00[YRI][hapmap]
rs6884276	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6899097	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72811045	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72811049	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9686940	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
6	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
10	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
11	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv883291	chr5:179755559-179818868	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv984575	chr5:179759624-179791220	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17080199	UNC5A	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179757000-179779000	Weak transcription	Esophagus	oesophagus
2	chr5:179759000-179770200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:179759200-179767800	Weak transcription	Fetal Intestine Small	intestine
4	chr5:179759800-179767200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:179760400-179767000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:179760600-179767000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:179761600-179770000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:179761600-179770200	Weak transcription	Right Ventricle	heart
9	chr5:179761800-179770400	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:179762200-179770400	Weak transcription	Hela-S3	cervix
11	chr5:179762600-179770200	Weak transcription	Placenta	Placenta
12	chr5:179763000-179767800	Weak transcription	NHLF	lung
13	chr5:179763000-179770000	Weak transcription	Brain Angular Gyrus	brain
14	chr5:179763000-179770000	Weak transcription	Fetal Lung	lung
15	chr5:179763000-179771400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:179763200-179770000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:179763600-179770000	Weak transcription	Brain Substantia Nigra	brain
18	chr5:179763600-179770200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:179763800-179769600	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:179764000-179770000	Weak transcription	Brain Germinal Matrix	brain
21	chr5:179764000-179778800	Weak transcription	Pancreas	Pancrea
22	chr5:179764200-179770000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:179764800-179767000	Enhancers	HSMM	muscle
24	chr5:179764800-179770000	Weak transcription	Brain Anterior Caudate	brain
25	chr5:179764800-179770000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:179765000-179768400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:179765000-179770000	Weak transcription	Adipose Nuclei	Adipose
28	chr5:179765000-179770000	Enhancers	Osteobl	bone
29	chr5:179765000-179770200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:179765000-179770200	Weak transcription	Fetal Brain Female	brain
31	chr5:179765000-179771000	Weak transcription	Left Ventricle	heart
32	chr5:179765000-179775000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:179765200-179768800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr5:179765200-179769800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:179765200-179770000	Weak transcription	Ovary	ovary
36	chr5:179765400-179770000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:179765400-179770000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:179765600-179767000	Enhancers	A549	lung
39	chr5:179765600-179767200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr5:179765600-179770000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:179765600-179770200	Weak transcription	HSMMtube	muscle
42	chr5:179765800-179767000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr5:179765800-179768200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:179766000-179768000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:179766000-179768400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr5:179766000-179770000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:179766600-179767000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr5:179766600-179767000	Genic enhancers	H1 Cell Line	embryonic stem cell
49	chr5:179766600-179767000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:179766600-179767000	Enhancers	Gastric	stomach

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