Variant report

Variant	rs11843974
Chromosome Location	chr13:96147663-96147664
allele	G/T
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:88)

rs_ID	r²[population]
rs10219866	0.91[ASN][1000 genomes]
rs11617639	0.89[ASN][1000 genomes]
rs11619150	0.86[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs12427460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12866697	0.87[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs12872431	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs12876693	0.86[ASN][1000 genomes]
rs12876913	0.90[ASN][1000 genomes]
rs1570903	0.87[CHB][hapmap];0.90[ASN][1000 genomes]
rs1570904	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1890373	0.86[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4322517	0.91[ASN][1000 genomes]
rs4335657	0.91[ASN][1000 genomes]
rs4351928	0.81[ASN][1000 genomes]
rs4387474	0.91[ASN][1000 genomes]
rs4394950	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402421	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4409957	0.87[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs4466958	0.87[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4547209	0.90[ASN][1000 genomes]
rs4564445	0.91[ASN][1000 genomes]
rs4564446	0.88[ASN][1000 genomes]
rs4587819	0.91[ASN][1000 genomes]
rs4609701	0.91[ASN][1000 genomes]
rs4771917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773907	0.91[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs4773908	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773909	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773910	0.90[ASN][1000 genomes]
rs4773911	0.90[ASN][1000 genomes]
rs4773912	0.87[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs57719175	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6492792	0.91[ASN][1000 genomes]
rs6492793	0.85[ASN][1000 genomes]
rs6492796	0.91[ASN][1000 genomes]
rs6492797	0.85[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs6492798	0.90[ASN][1000 genomes]
rs6492799	0.88[ASN][1000 genomes]
rs6492807	0.86[CHD][hapmap]
rs7139829	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7322391	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs7326265	0.91[ASN][1000 genomes]
rs7326546	0.85[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs7328468	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs7332888	0.91[ASN][1000 genomes]
rs7332917	0.87[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs7338647	0.87[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs7982486	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs7982563	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7984234	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs7990054	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs7992297	0.89[ASN][1000 genomes]
rs7995104	0.85[ASN][1000 genomes]
rs7995114	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7995959	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs8002444	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs8002639	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs877960	0.89[ASN][1000 genomes]
rs877961	0.90[ASN][1000 genomes]
rs877962	0.87[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs927786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs927787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs927788	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9302074	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs9302075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs946228	0.87[CHB][hapmap];0.91[CHD][hapmap]
rs946231	0.86[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs9516589	0.91[ASN][1000 genomes]
rs9516590	0.90[ASN][1000 genomes]
rs9524982	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs9524983	0.90[ASN][1000 genomes]
rs9524984	0.87[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs9524986	0.87[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs9524987	0.86[ASN][1000 genomes]
rs9524988	0.86[ASN][1000 genomes]
rs9524989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524991	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524992	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9524993	0.87[EUR][1000 genomes]
rs9524994	0.96[CEU][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9525017	0.84[CEU][hapmap]
rs9561880	0.87[ASN][1000 genomes]
rs9561885	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9590285	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs9590286	0.86[ASN][1000 genomes]
rs9590287	0.88[ASN][1000 genomes]
rs9590288	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043019	chr13:95924585-96152616	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv2752652	chr13:96059024-96181597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv900933	chr13:96138087-96215289	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11843974	FARP1	cis	cerebellum	SCAN
rs11843974	UGCGL2	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96145000-96152600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:96147200-96148800	Weak transcription	Esophagus	oesophagus

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