Variant report

Variant	rs7845676
Chromosome Location	chr8:39064549-39064550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10088458	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10088794	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10094572	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10095244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10095787	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10101558	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10101577	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10106195	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10108700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10110383	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10111607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10448058	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10448059	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10448062	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10808917	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11775433	0.95[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11775913	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11776234	0.85[CEU][hapmap]
rs11777233	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11780558	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11781014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781030	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11782591	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11783079	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11784002	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11784182	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11784263	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11786404	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11786558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12155966	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12543265	0.91[EUR][1000 genomes]
rs12546310	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12549006	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12675132	0.84[CEU][hapmap]
rs12682638	0.81[CEU][hapmap]
rs13439327	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13439544	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13439696	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13439859	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28505965	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28773215	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28788037	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28801793	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28812794	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28887526	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35815552	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3886041	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4133177	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4133178	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4349954	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4476977	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4513935	0.95[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4515515	0.80[CEU][hapmap];0.91[TSI][hapmap]
rs4537270	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4585712	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4587293	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4733913	0.80[CEU][hapmap]
rs4733982	0.81[AMR][1000 genomes]
rs4733983	0.92[EUR][1000 genomes]
rs4733985	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4733988	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4733991	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4733992	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4733994	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs55716826	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55759907	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55892966	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55977531	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56018942	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56093547	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56392075	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6474116	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6474117	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6980625	0.82[CHB][hapmap];0.87[TSI][hapmap]
rs6981906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6989252	0.81[CEU][hapmap]
rs6992204	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6996235	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6997278	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7000543	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7014889	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7016661	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs73606707	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73606713	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73606714	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73606745	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73606748	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73606767	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73606769	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73606771	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73606773	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73606793	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7822982	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7826829	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7843696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7843711	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9298561	0.93[EUR][1000 genomes]
rs9771995	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9801845	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015907	chr8:38967169-39718559	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv539550	chr8:38967169-39718559	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1027443	chr8:38993423-39181079	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv539551	chr8:38993423-39181079	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7845676	TM2D2	cis	cerebellum	SCAN
rs7845676	TM2D2	cis	parietal	SCAN
rs7845676	ASH2L	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39060400-39082600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr8:39062800-39064600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:39063000-39064800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr8:39063800-39064600	ZNF genes & repeats	Fetal Intestine Small	intestine
5	chr8:39063800-39065400	Enhancers	HepG2	liver
6	chr8:39064000-39064600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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