Variant report

Variant	rs4924617
Chromosome Location	chr15:42369548-42369549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11070356	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12148273	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17690109	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17690827	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17690899	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17691153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17747505	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17748059	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17748132	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1993069	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2412656	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28568280	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4923922	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4923923	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4923924	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4923925	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4923926	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4923927	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4923928	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924609	0.84[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes]
rs4924611	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924614	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924615	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924616	1.00[EUR][1000 genomes]
rs4924619	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924620	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7162019	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7165458	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7165460	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7166026	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166093	0.83[EUR][1000 genomes]
rs7166111	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166789	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7168863	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7173686	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176443	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7176459	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7177034	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs7180420	1.00[EUR][1000 genomes]
rs750051	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs750052	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs755599	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8029713	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1043641	chr15:42336584-42381240	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv904131	chr15:42343794-42390223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4924617	RTF1	cis	parietal	SCAN
rs4924617	CATSPER2P1	cis	parietal	SCAN
rs4924617	IVD	cis	parietal	SCAN
rs4924617	GPR176	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42363400-42371600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:42363600-42375800	Weak transcription	Esophagus	oesophagus
3	chr15:42366200-42369800	Weak transcription	Stomach Mucosa	stomach

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