Variant report

Variant	rs4849058
Chromosome Location	chr2:113103003-113103004
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	RAD21	chr2:113102980-113103639	MCF-7	breast:	n/a	n/a
2	GATA3	chr2:113102983-113103683	MCF-7	breast:	n/a	n/a
3	CTCF	chr2:113102986-113103638	MCF-7	breast:	n/a	n/a
4	MAX	chr2:113102811-113103678	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113031588..113034484-chr2:113102679..113104264,2	MCF-7	breast:
2	chr2:113016830..113017619-chr2:113102898..113103578,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236555	TF binding region
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10175234	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10203614	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10205897	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10439391	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11123135	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4299347	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4352239	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4392265	0.82[EUR][1000 genomes]
rs4419238	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4446076	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4542853	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4578863	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4630773	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62160223	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6542054	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6716010	0.81[EUR][1000 genomes]
rs6725933	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6726412	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71414636	0.81[AMR][1000 genomes]
rs7600338	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7601200	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7601888	0.84[AMR][1000 genomes];0.84[EUR][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	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4849058	RGPD8	cis	Muscle Skeletal	GTEx
rs4849058	ZC3H6	cis	brain	BrainEAC
rs4849058	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs4849058	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs4849058	RGPD8	cis	lung	GTEx
rs4849058	RGPD8	cis	Nerve Tibial	GTEx
rs4849058	RGPD8	cis	Artery Tibial	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113085800-113103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:113089400-113103400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:113090000-113103400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:113090000-113103400	Weak transcription	Spleen	Spleen
5	chr2:113098400-113104400	Weak transcription	Fetal Kidney	kidney
6	chr2:113101400-113104200	Weak transcription	Right Atrium	heart
7	chr2:113102400-113105000	Weak transcription	NHLF	lung
8	chr2:113102600-113103600	Flanking Active TSS	HepG2	liver
9	chr2:113102600-113105600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:113102800-113103400	Active TSS	Placenta	Placenta

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