Variant report

Variant	rs13239559
Chromosome Location	chr7:126753700-126753701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10464688	0.82[CHB][hapmap]
rs1111183	1.00[ASW][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs11563356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11563716	0.85[JPT][hapmap]
rs11563730	0.83[GIH][hapmap]
rs12538500	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap]
rs12706759	1.00[ASW][hapmap]
rs12706761	0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12706762	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13234354	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13244682	0.87[YRI][hapmap]
rs1361961	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1419442	1.00[ASW][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs1557644	1.00[ASW][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1557645	0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17863206	0.88[YRI][hapmap]
rs17869426	0.87[YRI][hapmap]
rs2023640	1.00[ASW][hapmap]
rs2188187	1.00[ASW][hapmap]
rs2299531	0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2299532	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2299536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2299546	1.00[LWK][hapmap]
rs4728065	0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs886001	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs916608	0.88[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs916610	0.83[GIH][hapmap]
rs929172	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs950527	0.87[YRI][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	nsv831121	chr7:126593363-126774413	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv889189	chr7:126699088-126963028	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2761367	chr7:126717157-126865324	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv518034	chr7:126750322-126753750	Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv971570	chr7:126753415-126757393	Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13239559	TMEM209	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:126753400-126755400	Enhancers	HUES48 Cell Line	embryonic stem cell

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