Variant report

Variant	rs17080196
Chromosome Location	chr5:179762405-179762406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179760391-179762871	U87	brain:	n/a	n/a
2	POLR2A	chr5:179761918-179762865	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179761022..179762666-chr5:179778358..179780120,2	MCF-7	breast:
2	chr5:179755365..179757615-chr5:179761406..179763311,3	K562	blood:
3	chr5:179761366..179762907-chr5:179778536..179780759,2	MCF-7	breast:
4	chr5:179761126..179762815-chr5:179764028..179766885,2	MCF-7	breast:

Variant related genes	Relation type
GFPT2	TF binding region
ENSG00000131459	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1078646	0.87[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs1559114	0.88[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs17080199	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];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235511	0.81[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs4566752	0.88[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs4700736	0.81[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs4700943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404950	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404953	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62404956	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62404958	0.88[ASN][1000 genomes]
rs62404959	0.89[ASN][1000 genomes]
rs62406364	0.83[ASN][1000 genomes]
rs6601110	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6859159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864729	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871454	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884276	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6899097	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72811045	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811049	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686940	0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17080196	UNC5A	cis	cerebellum	SCAN
rs17080196	MXD3	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179741600-179762600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:179744000-179766600	Weak transcription	Gastric	stomach
3	chr5:179757000-179779000	Weak transcription	Esophagus	oesophagus
4	chr5:179757800-179765600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:179759000-179762800	Weak transcription	Pancreas	Pancrea
6	chr5:179759000-179764600	Weak transcription	Left Ventricle	heart
7	chr5:179759000-179766600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:179759000-179770200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:179759200-179767800	Weak transcription	Fetal Intestine Small	intestine
10	chr5:179759600-179762800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:179759600-179766600	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr5:179759800-179766000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:179759800-179767200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:179760000-179765600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:179760000-179765800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:179760200-179765400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:179760400-179765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:179760400-179765800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:179760400-179767000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:179760600-179764200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:179760600-179764800	Strong transcription	Brain Anterior Caudate	brain
22	chr5:179760600-179765000	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr5:179760600-179765400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:179760600-179765600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr5:179760600-179765800	Strong transcription	Fetal Muscle Leg	muscle
26	chr5:179760600-179766000	Strong transcription	Fetal Stomach	stomach
27	chr5:179760600-179767000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:179760800-179763000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:179760800-179763200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:179760800-179763600	Strong transcription	Brain Substantia Nigra	brain
31	chr5:179760800-179764000	Strong transcription	Brain Germinal Matrix	brain
32	chr5:179760800-179764800	Strong transcription	Brain Cingulate Gyrus	brain
33	chr5:179760800-179765200	Strong transcription	Ovary	ovary
34	chr5:179760800-179765400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:179760800-179765600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr5:179761000-179762800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:179761000-179763000	Strong transcription	Brain Angular Gyrus	brain
38	chr5:179761000-179763800	Strong transcription	Brain Hippocampus Middle	brain
39	chr5:179761000-179765000	Strong transcription	Fetal Brain Female	brain
40	chr5:179761000-179765800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr5:179761200-179762600	Genic enhancers	A549	lung
42	chr5:179761200-179765000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:179761200-179766600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr5:179761400-179762600	Strong transcription	Placenta	Placenta
45	chr5:179761400-179762800	Strong transcription	Aorta	Aorta
46	chr5:179761400-179763000	Strong transcription	Fetal Lung	lung
47	chr5:179761400-179763000	Strong transcription	Lung	lung
48	chr5:179761600-179762600	Weak transcription	HSMMtube	muscle
49	chr5:179761600-179764800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:179761600-179765000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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