Variant report

Variant	rs4238964
Chromosome Location	chr16:72175156-72175157
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10400963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1050362	0.81[YRI][hapmap]
rs10852511	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11075922	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11075924	0.90[JPT][hapmap]
rs11643192	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12325142	0.81[YRI][hapmap]
rs12325266	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12444701	0.83[ASN][1000 genomes]
rs12449073	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12708928	0.80[CHD][hapmap];0.81[YRI][hapmap]
rs12928732	0.81[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12929749	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12932845	0.86[JPT][hapmap]
rs12933838	0.89[ASN][1000 genomes]
rs12935232	0.82[ASN][1000 genomes]
rs13334151	0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs16973716	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070937	0.86[JPT][hapmap]
rs2070939	0.85[JPT][hapmap]
rs2072142	0.81[YRI][hapmap]
rs2074626	0.84[JPT][hapmap];0.81[YRI][hapmap]
rs2074627	0.80[CHD][hapmap];0.81[YRI][hapmap]
rs2240243	0.81[YRI][hapmap]
rs2241411	0.90[JPT][hapmap]
rs2241412	0.81[CHD][hapmap];0.88[YRI][hapmap]
rs2288002	0.85[JPT][hapmap]
rs2550868	0.85[JPT][hapmap]
rs28432692	0.89[ASN][1000 genomes]
rs34714490	0.90[ASN][1000 genomes]
rs35460163	0.90[ASN][1000 genomes]
rs3764312	0.85[JPT][hapmap]
rs3812984	0.90[JPT][hapmap]
rs3812986	0.85[JPT][hapmap]
rs3812987	0.82[ASN][1000 genomes]
rs3844425	0.87[GIH][hapmap];0.95[JPT][hapmap]
rs3852782	0.95[JPT][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs3852784	0.95[JPT][hapmap];0.81[YRI][hapmap]
rs3852788	0.84[ASN][1000 genomes]
rs3902135	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs3909541	0.90[JPT][hapmap]
rs3909542	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3909543	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788609	0.95[JPT][hapmap];0.81[YRI][hapmap]
rs4788610	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs56960650	0.87[ASN][1000 genomes]
rs57186116	0.84[ASN][1000 genomes]
rs6499562	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7184169	0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs7188058	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7190995	0.81[YRI][hapmap]
rs7191127	0.81[YRI][hapmap]
rs7192848	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7198572	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs7200003	0.80[ASN][1000 genomes]
rs7201225	0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7201643	0.86[JPT][hapmap]
rs7203426	0.85[JPT][hapmap]
rs7203821	0.86[JPT][hapmap]
rs7940	0.90[JPT][hapmap]
rs8044555	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs8044868	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8045481	0.85[ASN][1000 genomes]
rs8050238	0.82[ASN][1000 genomes]
rs8051882	0.80[CHD][hapmap];0.88[YRI][hapmap]
rs8052338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8052408	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8059437	0.90[JPT][hapmap]
rs8061282	0.83[ASN][1000 genomes]
rs8061459	0.83[ASN][1000 genomes]
rs9302635	0.87[LWK][hapmap];0.82[YRI][hapmap]
rs9923344	0.87[ASN][1000 genomes]
rs9924964	0.84[JPT][hapmap]
rs9926156	0.93[YRI][hapmap]
rs9927526	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs9928157	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs9932951	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs9933009	0.87[ASN][1000 genomes]
rs9936642	0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.85[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4238964	FAM65A	cis	cerebellum	SCAN
rs4238964	DHODH	cis	cerebellum	SCAN
rs4238964	DHX38	cis	multi-tissue	Pritchard
rs4238964	SLC7A6OS	cis	parietal	SCAN
rs4238964	HP	cis	cerebellum	SCAN
rs4238964	VPS4A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72172400-72193000	Weak transcription	HepG2	liver

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