Variant report

Variant	rs5960738
Chromosome Location	chrX:56588095-56588096
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12690340	1.00[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs1387716	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs1927222	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs2130431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5914700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs5914709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs5914710	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[TSI][hapmap]
rs5914776	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs5914778	0.91[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs5914779	0.83[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs5960204	0.82[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap]
rs5960754	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs5960785	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6612559	0.82[YRI][hapmap]
rs6612632	0.83[ASW][hapmap];0.82[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	esv2756104	chrX:56292362-56824154	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS 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 target site	12 gene(s)	inside rSNPs	diseases
7	esv2754937	chrX:56482424-56851953	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv6916	chrX:56553895-56598754	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5960738	SPIN-2	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:56587600-56588800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chrX:56587600-56589200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chrX:56588000-56589200	Enhancers	Dnd41	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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