Variant report

Variant	rs13140128
Chromosome Location	chr4:8529812-8529813
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8500815..8505571-chr4:8524859..8530536,4	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16842480	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16842483	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs16842486	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs16842498	0.89[ASN][1000 genomes]
rs16842557	0.87[ASN][1000 genomes]
rs16842560	0.86[ASN][1000 genomes]
rs16842563	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3103082	0.94[ASN][1000 genomes]
rs34055610	0.85[AMR][1000 genomes]
rs4247232	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4247233	0.90[ASN][1000 genomes]
rs4259044	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4358384	0.94[ASN][1000 genomes]
rs4619877	0.88[ASN][1000 genomes]
rs4696692	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4696693	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4696695	0.91[ASN][1000 genomes]
rs4696696	0.90[ASN][1000 genomes]
rs4696838	0.89[ASN][1000 genomes]
rs55765509	0.90[ASN][1000 genomes]
rs55789011	0.89[ASN][1000 genomes]
rs55977448	0.88[ASN][1000 genomes]
rs56053534	0.88[ASN][1000 genomes]
rs61258495	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62287446	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62287455	0.87[ASN][1000 genomes]
rs869600	0.90[ASN][1000 genomes]
rs869602	0.94[ASN][1000 genomes]
rs883607	0.86[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv4224	chr4:8503727-8546462	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv878611	chr4:8512889-8534283	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13140128	C4orf23	cis	cerebellum	SCAN
rs13140128	C4orf23	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8528200-8530200	Weak transcription	HSMMtube	muscle
2	chr4:8528200-8534000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:8528200-8535600	Weak transcription	Ovary	ovary
4	chr4:8528400-8530400	Weak transcription	NHLF	lung
5	chr4:8528400-8533600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:8528600-8530200	Weak transcription	HSMM	muscle
7	chr4:8528600-8530200	Weak transcription	NHDF-Ad	bronchial
8	chr4:8529400-8532600	Weak transcription	Placenta	Placenta

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