Variant report

Variant	rs5960112
Chromosome Location	chrX:55930768-55930769
allele	C/T
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	POLR2A	chrX:55930717-55930812	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000227486	TF binding region
ENSG00000252961	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1007153	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1325573	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1473760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1591015	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs2375466	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4826281	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826283	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826287	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4826413	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5913857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs5914428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs5914432	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs5914433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5914436	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs5914440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5960093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5960123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]
rs6611431	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs6612417	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs913440	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3384643	chrX:55919980-55939813	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
2	esv2752678	chrX:55930768-56851953	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2753382	chrX:55930768-56851953	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2754448	chrX:55930768-56851953	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2755974	chrX:55930768-56851953	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv432333	chrX:55930768-56851953	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5960112	RRAGB	cis	lymphoblastoid	seeQTL
rs5960112	SPIN-2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:55930200-55932200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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