Variant report

Variant	rs16988539
Chromosome Location	chrX:29452027-29452028
allele	C/T
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:18)

rs_ID	r²[population]
rs11798204	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12007907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12014776	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12841004	1.00[CHB][hapmap]
rs16988537	1.00[TSI][hapmap]
rs16988538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16988558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16988604	1.00[CHB][hapmap]
rs16988634	1.00[CHB][hapmap]
rs5971928	1.00[TSI][hapmap]
rs5972128	0.81[YRI][hapmap]
rs6526860	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6526868	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7052807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7065816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs714723	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs715329	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs721603	1.00[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432292	chrX:29109744-29845461	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv531754	chrX:29147023-29533186	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv531766	chrX:29225499-29928832	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv948944	chrX:29398264-29902917	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869450	chrX:29433295-29940875	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16988539	TMPRSS3	trans	lymphoblastoid	seeQTL

Chromatin state (count:0 , 50 per page) page:

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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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