Variant report

Variant	rs28478989
Chromosome Location	chr5:179500185-179500186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr5:179498817-179500284	H1-hESC	embryonic stem cell:	n/a	chr5:179499224-179499236 chr5:179499223-179499234 chr5:179499201-179499210

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179285802..179287373-chr5:179498927..179500668,2	MCF-7	breast:
2	chr5:179333483..179336281-chr5:179498634..179500565,2	K562	blood:
3	chr5:179333483..179336002-chr5:179498536..179500364,3	K562	blood:
4	chr5:179404319..179405843-chr5:179497809..179500320,2	K562	blood:
5	chr5:179499106..179500693-chr5:179512372..179515293,2	K562	blood:
6	chr5:179499305..179501402-chr5:179506576..179508838,2	K562	blood:
7	chr5:179285987..179287986-chr5:179498943..179500555,2	K562	blood:
8	chr5:179246093..179248273-chr5:179497691..179500264,2	MCF-7	breast:
9	chr5:179332761..179336643-chr5:179497180..179500753,5	MCF-7	breast:
10	chr5:179285948..179288985-chr5:179497401..179500729,4	K562	blood:
11	chr5:179232651..179234632-chr5:179498072..179500275,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNF130	TF binding region
ENSG00000113269	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000253480	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000245317	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10067073	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10072792	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479558	0.87[EUR][1000 genomes]
rs10479559	0.87[EUR][1000 genomes]
rs10479560	0.84[EUR][1000 genomes]
rs1110145	0.84[EUR][1000 genomes]
rs11952090	0.84[EUR][1000 genomes]
rs12521819	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13354862	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1345085	0.87[EUR][1000 genomes]
rs1345087	0.87[EUR][1000 genomes]
rs1345088	0.87[EUR][1000 genomes]
rs58286692	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59150995	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59668758	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60044157	0.90[EUR][1000 genomes]
rs60388708	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	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
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	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
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	esv3396669	chr5:179497796-179500194	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	esv3340100	chr5:179497871-179500719	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28478989	RNF130	cis	Whole Blood	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179499200-179500200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:179499400-179517000	Weak transcription	Right Atrium	heart
3	chr5:179499600-179501000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:179499600-179501400	Weak transcription	Fetal Heart	heart
5	chr5:179499600-179508200	Weak transcription	Right Ventricle	heart
6	chr5:179499800-179500200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr5:179499800-179500200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:179499800-179500800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:179499800-179502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:179500000-179500400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr5:179500000-179501400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:179500000-179501800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:179500000-179502200	Weak transcription	Liver	Liver
14	chr5:179500000-179502200	Weak transcription	Fetal Brain Male	brain

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