Variant report

Variant	rs2860346
Chromosome Location	chr16:72592309-72592310
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10852514	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11075935	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11646282	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11862324	0.90[EUR][1000 genomes]
rs11865896	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12149680	0.87[EUR][1000 genomes]
rs12598598	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13333122	0.85[GIH][hapmap]
rs1429072	0.80[AMR][1000 genomes]
rs16970900	0.84[EUR][1000 genomes]
rs16970908	0.80[EUR][1000 genomes]
rs1864231	0.90[EUR][1000 genomes]
rs1991530	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2079161	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2158265	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2158266	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2158268	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28677977	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2914769	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2914771	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2914774	0.80[AMR][1000 genomes]
rs2914777	0.80[AMR][1000 genomes]
rs2914779	0.80[AMR][1000 genomes]
rs292936	0.96[YRI][hapmap]
rs2967240	0.81[AMR][1000 genomes]
rs4410082	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56152199	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62051139	0.90[EUR][1000 genomes]
rs7194533	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7204631	0.91[EUR][1000 genomes]
rs7205109	0.85[GIH][hapmap];0.88[MEX][hapmap]
rs8046070	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8047866	0.82[EUR][1000 genomes]
rs8048832	0.88[GIH][hapmap];0.85[MKK][hapmap]
rs8057278	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8060607	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs806732	0.81[GIH][hapmap]
rs806733	0.85[GIH][hapmap]
rs806739	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9302637	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9930813	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1067525	chr16:72342110-72602796	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv542948	chr16:72342110-72602796	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1055807	chr16:72418417-72614308	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv523524	chr16:72464460-72635674	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1055142	chr16:72473520-72627783	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv542950	chr16:72473520-72627783	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv530712	chr16:72499171-72744114	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1064928	chr16:72509626-72627783	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1065173	chr16:72509626-72693970	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv542951	chr16:72509626-72693970	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv518234	chr16:72544447-72635674	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv1064027	chr16:72559417-72656702	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv1063049	chr16:72577004-72887111	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
18	nsv542952	chr16:72577004-72887111	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2860346	PRMT7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72584000-72594600	Weak transcription	Primary B cells from cord blood	blood
2	chr16:72591800-72593000	Enhancers	Duodenum Mucosa	Duodenum
3	chr16:72592200-72592600	Enhancers	Stomach Mucosa	stomach

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