Variant report

Variant	rs5960817
Chromosome Location	chrX:56859580-56859581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10521485	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12690340	0.80[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap]
rs1927222	0.80[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.82[MKK][hapmap]
rs5914036	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs5914037	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs5914776	0.83[CHD][hapmap]
rs5914778	0.83[CHD][hapmap];0.89[GIH][hapmap];0.80[MKK][hapmap]
rs5914779	0.83[ASW][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.91[YRI][hapmap]
rs5914874	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs5960204	0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs5960235	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs6612632	0.83[ASW][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.91[YRI][hapmap]
rs6612746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs912956	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758569	chrX:56739069-56887748	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2758867	chrX:56739069-56887748	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5960817	SPIN-2	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:56858400-56860400	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chrX:56859200-56860200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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