Variant report

Variant	rs6521388
Chromosome Location	chrX:56345127-56345128
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1033565	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap]
rs12862304	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2375630	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2375631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs3747284	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap]
rs4826308	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs5913918	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs5960155	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap]
rs5960668	0.82[YRI][hapmap]
rs5960669	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap]
rs6521375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs6521376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs6611493	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap]
rs6612506	0.80[CEU][hapmap];0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv534648	chrX:56306570-56395419	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv3392306	chrX:56342980-56430729	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
9	esv3350483	chrX:56342980-56445360	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6521388	SPIN-2	cis	multi-tissue	Pritchard
rs6521388	RRAGB	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:56344800-56345600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chrX:56345000-56346600	ZNF genes & repeats	iPS-18 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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