Variant report

Variant	rs4144102
Chromosome Location	chr10:26568705-26568706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10508715	0.89[TSI][hapmap]
rs10828968	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10828969	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11015014	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11015024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11015026	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11015028	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11594057	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11594128	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12243037	0.81[MEX][hapmap];0.89[TSI][hapmap]
rs12247267	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12248143	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12250822	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12414701	0.82[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12572822	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1330572	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1330581	0.82[CHB][hapmap];0.82[GIH][hapmap]
rs1330582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1335547	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1831432	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1935996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1999241	0.82[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2017306	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2236418	0.89[TSI][hapmap]
rs2368159	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2368160	0.82[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs2839670	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs2839671	0.89[TSI][hapmap]
rs3781106	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781109	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3781111	0.84[ASN][1000 genomes]
rs3781112	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3781113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781114	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3824694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3847379	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3847380	0.83[ASN][1000 genomes]
rs4747547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4747548	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4747549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4747550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4747552	0.82[ASN][1000 genomes]
rs4747553	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4749100	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4749101	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4749102	0.82[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4749103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4749105	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4749107	0.82[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4749108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4749109	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4749110	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4749111	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55878324	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56086837	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56405990	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57685594	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838363	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61839388	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6482548	0.82[ASN][1000 genomes]
rs6482550	0.82[ASN][1000 genomes]
rs6482555	0.81[ASN][1000 genomes]
rs7067571	0.82[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7073119	0.82[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7074235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7074897	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7076544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7080128	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7089218	0.81[ASN][1000 genomes]
rs7095327	0.82[ASN][1000 genomes]
rs7893400	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7900976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7902107	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7906725	0.82[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7909127	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7913676	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7918935	0.81[ASN][1000 genomes]
rs8190706	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8190748	0.82[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs8190754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8190756	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8190757	0.81[ASN][1000 genomes]
rs8190764	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs8190780	0.83[ASN][1000 genomes]
rs8190782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8190809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs882138	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs913962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913963	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913964	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs913965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs989118	0.82[EUR][1000 genomes]
rs992990	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs994502	0.93[TSI][hapmap]

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
rs4144102	COMMD3	cis	parietal	SCAN
rs4144102	THNSL1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26559000-26576600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr10:26564000-26569200	Weak transcription	Fetal Brain Male	brain
3	chr10:26564000-26581800	Weak transcription	Brain Anterior Caudate	brain
4	chr10:26566400-26579600	Weak transcription	Brain Germinal Matrix	brain
5	chr10:26566600-26570000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:26567800-26569200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr10:26568400-26569000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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