Variant report

Variant	rs7906725
Chromosome Location	chr10:26562897-26562898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11015014	0.81[ASN][1000 genomes]
rs11015015	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11015024	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11015026	0.83[ASN][1000 genomes]
rs11015028	0.82[ASN][1000 genomes]
rs11594057	0.82[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11594128	0.83[ASN][1000 genomes]
rs12241667	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12245460	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12265385	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12414701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330581	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1330582	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1335547	0.81[ASN][1000 genomes]
rs1888251	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1935996	0.80[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1999241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150158	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2368159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2368160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781106	0.81[ASN][1000 genomes]
rs3781108	0.82[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3781109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781111	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781113	0.82[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3781114	0.84[ASN][1000 genomes]
rs3824694	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3847378	0.82[EUR][1000 genomes]
rs3847379	0.82[ASN][1000 genomes]
rs3847380	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4144102	0.82[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4747547	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4747548	0.80[ASN][1000 genomes]
rs4747549	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4747550	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4749100	0.81[ASN][1000 genomes]
rs4749101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4749102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4749103	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4749105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4749107	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];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4749108	0.82[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4749109	0.82[ASN][1000 genomes]
rs4749112	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4749113	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55878324	0.82[ASN][1000 genomes]
rs56086837	0.82[ASN][1000 genomes]
rs56405990	0.84[ASN][1000 genomes]
rs57685594	0.82[ASN][1000 genomes]
rs61839388	0.82[ASN][1000 genomes]
rs6482548	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482550	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7068091	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7071922	0.80[EUR][1000 genomes]
rs7073119	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];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074235	0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7076544	0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs7079553	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7079848	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7080952	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7089218	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7091779	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7095327	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893400	0.84[ASN][1000 genomes]
rs7900739	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7900976	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7902107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7909127	0.84[ASN][1000 genomes]
rs7913676	0.82[ASN][1000 genomes]
rs7918935	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8190678	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8190683	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8190704	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8190706	0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs8190748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8190754	0.82[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs8190756	0.83[ASN][1000 genomes]
rs8190757	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8190764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8190780	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8190782	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs8190809	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs882139	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs913962	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs913963	0.84[ASN][1000 genomes]
rs913964	0.82[ASN][1000 genomes]
rs913965	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs992990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7906725	ABI1	cis	parietal	SCAN
rs7906725	THNSL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26558000-26563200	Weak transcription	Brain Anterior Caudate	brain
2	chr10:26559000-26563400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr10:26559000-26563400	Weak transcription	Fetal Brain Female	brain
4	chr10:26559000-26576600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:26560200-26563000	Weak transcription	Brain Germinal Matrix	brain
6	chr10:26562400-26565600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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