Variant report

Variant	rs1559113
Chromosome Location	chr5:179751390-179751391
allele	A/G
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	RCOR1	chr5:179750769-179751593	IMR90	lung:	n/a	n/a
2	POLR2A	chr5:179750977-179751399	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:179750833-179752935	U87	brain:	n/a	n/a
4	POLR2A	chr5:179750823-179751555	U87	brain:	n/a	n/a
5	CEBPB	chr5:179751031-179751393	A549	lung:	n/a	chr5:179751144-179751155 chr5:179751145-179751156
6	MAFK	chr5:179750954-179751575	IMR90	lung:	n/a	n/a
7	REST	chr5:179751038-179751450	ECC-1	luminal epithelium:	n/a	n/a
8	REST	chr5:179751014-179751480	A549	lung:	n/a	n/a
9	REST	chr5:179751032-179751448	MCF-7	breast:	n/a	n/a
10	E2F4	chr5:179751147-179751427	MCF10A-Er-Src	breast:	n/a	n/a
11	MXI1	chr5:179750737-179751927	IMR90	lung:	n/a	n/a
12	MAFK	chr5:179751317-179751498	HepG2	liver:	n/a	n/a
13	REST	chr5:179750971-179751396	PFSK-1	brain:	n/a	n/a
14	REST	chr5:179750920-179751419	PFSK-1	brain:	n/a	n/a
15	REST	chr5:179751012-179751471	Hela-S3	cervix:	n/a	n/a
16	REST	chr5:179750980-179751460	PFSK-1	brain:	n/a	n/a
17	REST	chr5:179751010-179751449	HL-60	blood:	n/a	n/a
18	REST	chr5:179750889-179751446	U87	brain:	n/a	n/a
19	POLR2A	chr5:179750839-179752549	U87	brain:	n/a	n/a
20	POLR2A	chr5:179750819-179751555	U87	brain:	n/a	n/a
21	REST	chr5:179751001-179751464	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
GFPT2	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2892152	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs3805705	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs3828687	0.86[EUR][1000 genomes]
rs62404923	0.83[EUR][1000 genomes]
rs62404927	0.84[EUR][1000 genomes]
rs62404934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6872946	0.89[EUR][1000 genomes]
rs6874433	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6877489	0.82[ASW][hapmap]
rs6878656	0.84[EUR][1000 genomes]
rs6879034	0.92[EUR][1000 genomes]
rs73343449	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1559113	PDLIM7	cis	cerebellum	SCAN
rs1559113	MAPK9	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
2	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:179727000-179755800	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:179727200-179757400	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr5:179727200-179757400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:179727400-179757600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:179727600-179757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:179728600-179761400	Weak transcription	Aorta	Aorta
9	chr5:179731600-179755600	Weak transcription	Fetal Brain Female	brain
10	chr5:179736800-179751800	Weak transcription	Left Ventricle	heart
11	chr5:179738000-179758000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:179738200-179755600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:179739600-179761200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:179740400-179757400	Weak transcription	NHLF	lung
15	chr5:179740600-179757600	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr5:179741200-179754000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:179741600-179756000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:179741600-179757600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:179741600-179762600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:179741800-179758200	Weak transcription	Fetal Intestine Small	intestine
21	chr5:179742000-179757400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:179742600-179757800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr5:179743200-179761000	Weak transcription	Right Ventricle	heart
24	chr5:179743400-179754200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:179743400-179758200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:179743800-179756400	Weak transcription	Colonic Mucosa	Colon
27	chr5:179743800-179757400	Weak transcription	Fetal Lung	lung
28	chr5:179744000-179766600	Weak transcription	Gastric	stomach
29	chr5:179746000-179760800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:179746000-179761400	Weak transcription	Right Atrium	heart
31	chr5:179748200-179752800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:179748400-179753200	Strong transcription	Fetal Stomach	stomach
33	chr5:179749200-179757400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:179750000-179752600	Weak transcription	Fetal Heart	heart
35	chr5:179750200-179751600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:179750200-179752400	Enhancers	Brain Hippocampus Middle	brain
37	chr5:179750200-179752600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:179750200-179752600	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr5:179750200-179752800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:179750200-179756600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:179750200-179757400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:179750400-179751800	Enhancers	Brain Angular Gyrus	brain
43	chr5:179750400-179752200	Genic enhancers	NH-A	brain
44	chr5:179750400-179752400	Enhancers	Brain Germinal Matrix	brain
45	chr5:179750400-179752400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr5:179750600-179751400	Enhancers	Placenta	Placenta
47	chr5:179750600-179751800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:179750600-179751800	Genic enhancers	A549	lung
49	chr5:179750600-179752000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:179750600-179752000	Genic enhancers	Osteobl	bone

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