Variant report

Variant	rs5971580
Chromosome Location	chrX:31601557-31601558
allele	A/G
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]
rs1344082	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs4370684	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs5972397	0.80[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs5972404	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs5972413	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5972417	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5972426	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6527098	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs6527103	0.91[JPT][hapmap]
rs6628613	0.91[JPT][hapmap]
rs6631322	1.00[JPT][hapmap]
rs6631323	1.00[JPT][hapmap]
rs6631343	0.88[CHB][hapmap]
rs6631346	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap]
rs6631348	1.00[JPT][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	nsv869389	chrX:31207964-31963300	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active 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	7 gene(s)	inside rSNPs	diseases
2	nsv481964	chrX:31270220-31672751	Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv531098	chrX:31462522-31824884	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv481719	chrX:31470100-31807209	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv497882	chrX:31537077-31619941	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv481814	chrX:31566314-32058570	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv521457	chrX:31580537-31634092	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv481764	chrX:31587315-31944285	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5971580	PLEK	trans	brain	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:31599600-31606200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chrX:31599600-31606400	Weak transcription	NHEK	skin
3	chrX:31599800-31603600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chrX:31600000-31603800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chrX:31601000-31601600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chrX:31601200-31601600	Enhancers	HMEC	breast

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Input of quick search could be:

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

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