Variant report

Variant	rs7706789
Chromosome Location	chr5:147286458-147286459
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	MAX	chr5:147285903-147286548	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:147286384-147286513	Gliobla	brain:	n/a	n/a
3	MAX	chr5:147286387-147286660	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr5:147285929-147286593	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA3	chr5:147285782-147286488	SK-N-SH	brain:	n/a	chr5:147286416-147286424
6	RCOR1	chr5:147285971-147286486	Hela-S3	cervix:	n/a	n/a
7	MYC	chr5:147285939-147286614	MCF10A-Er-Src	breast:	n/a	n/a
8	GATA3	chr5:147285757-147286485	SK-N-SH	brain:	n/a	chr5:147286416-147286424
9	JUND	chr5:147285975-147286476	Hela-S3	cervix:	n/a	chr5:147286144-147286153

Variant related genes	Relation type
C5orf46	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10477355	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11956228	0.80[EUR][1000 genomes]
rs11958481	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1432973	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1432974	0.94[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1549204	0.80[YRI][hapmap]
rs17107413	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17107421	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17625543	0.80[EUR][1000 genomes]
rs17703848	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1835968	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1835969	0.93[ASN][1000 genomes]
rs2304067	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6580506	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6859879	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6862197	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73263247	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7722416	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7722926	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7706789	SYNPO	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147273400-147289000	Weak transcription	Left Ventricle	heart
2	chr5:147283400-147286800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:147283600-147286800	Enhancers	HMEC	breast
4	chr5:147284200-147291000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:147285000-147286800	Enhancers	Fetal Heart	heart
6	chr5:147285400-147286800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr5:147285600-147286800	Enhancers	Hela-S3	cervix
8	chr5:147285800-147286600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:147285800-147286600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:147285800-147286600	Enhancers	HSMM	muscle
11	chr5:147285800-147286800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:147285800-147286800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:147285800-147286800	Enhancers	Placenta	Placenta
14	chr5:147286000-147286600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:147286000-147286600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:147286000-147286600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:147286000-147286600	Enhancers	Gastric	stomach
18	chr5:147286000-147286600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr5:147286000-147286600	Flanking Active TSS	NHEK	skin
20	chr5:147286000-147286800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:147286000-147286800	Enhancers	Pancreas	Pancrea
22	chr5:147286200-147286600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:147286200-147286600	Enhancers	Right Ventricle	heart
24	chr5:147286200-147286600	Enhancers	HSMMtube	muscle
25	chr5:147286200-147286600	Enhancers	NH-A	brain
26	chr5:147286400-147286600	ZNF genes & repeats	Aorta	Aorta
27	chr5:147286400-147286600	Enhancers	Brain Substantia Nigra	brain
28	chr5:147286400-147286600	Flanking Active TSS	Osteobl	bone
29	chr5:147286400-147286800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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