Variant report

Variant	rs3909541
Chromosome Location	chr16:72201119-72201120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1006436	0.89[ASN][1000 genomes]
rs10400963	0.90[JPT][hapmap]
rs1050363	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10852511	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11075924	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11643192	0.86[GIH][hapmap];0.95[JPT][hapmap]
rs12325266	0.95[JPT][hapmap]
rs12449073	0.90[JPT][hapmap]
rs12918956	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12928365	0.80[ASN][1000 genomes]
rs12930285	0.91[ASN][1000 genomes]
rs12932845	0.80[ASW][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs16973716	0.85[JPT][hapmap]
rs2070937	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2070939	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2241411	0.91[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs2288000	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs2288002	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2550868	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs3812984	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812986	0.90[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3844425	0.80[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844426	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3852782	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3852784	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852786	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3852787	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3909542	0.88[ASN][1000 genomes]
rs4238964	0.90[JPT][hapmap]
rs4788461	0.81[AMR][1000 genomes]
rs4788464	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4788609	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4788610	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6499562	0.85[JPT][hapmap]
rs6499563	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6499564	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7186155	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7192848	0.95[JPT][hapmap]
rs7193559	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7197020	0.86[ASN][1000 genomes]
rs7200003	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7201225	0.95[GIH][hapmap];0.95[JPT][hapmap]
rs7201643	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs7203426	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7203821	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs7940	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs8044868	0.85[JPT][hapmap]
rs8052338	0.90[JPT][hapmap]
rs8052408	0.85[JPT][hapmap]
rs8059437	0.80[ASW][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs8060770	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9924964	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs9927526	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9928157	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs9932951	0.91[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs9936642	0.95[GIH][hapmap];0.95[JPT][hapmap]
rs9936784	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	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
6	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3909541	FAM65A	cis	cerebellum	SCAN
rs3909541	HP	cis	multi-tissue	Pritchard
rs3909541	HPR	cis	parietal	SCAN
rs3909541	DHX38	cis	Lymphoblastoid	GTEx
rs3909541	DHX38	cis	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72194600-72206200	Weak transcription	Primary B cells from cord blood	blood
2	chr16:72196600-72201200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr16:72199000-72203600	Weak transcription	Fetal Brain Female	brain
4	chr16:72199000-72204400	Weak transcription	Fetal Brain Male	brain

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