Variant report

Variant	rs2890046
Chromosome Location	chr14:32334616-32334617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10129419	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10130764	0.96[ASN][1000 genomes]
rs10135411	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10136892	0.90[ASN][1000 genomes]
rs10141141	0.90[ASN][1000 genomes]
rs10148852	0.80[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs10150448	0.92[ASN][1000 genomes]
rs10152018	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10152063	0.83[ASN][1000 genomes]
rs10348	0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11156713	0.85[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs11156714	0.84[ASN][1000 genomes]
rs11156716	0.91[ASN][1000 genomes]
rs11156717	0.94[ASN][1000 genomes]
rs1129622	0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1129623	0.91[ASN][1000 genomes]
rs11627083	0.81[ASN][1000 genomes]
rs12431828	0.86[ASN][1000 genomes]
rs12432404	0.83[ASN][1000 genomes]
rs12589862	0.85[CHB][hapmap]
rs1572190	0.92[ASN][1000 genomes]
rs1889387	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1953270	0.82[ASN][1000 genomes]
rs1959071	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs1959072	0.91[ASN][1000 genomes]
rs1959073	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1959074	0.95[ASN][1000 genomes]
rs1959075	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2039484	0.85[ASN][1000 genomes]
rs2039485	0.84[ASN][1000 genomes]
rs2378970	0.92[ASN][1000 genomes]
rs28639476	0.83[ASN][1000 genomes]
rs35943743	0.91[ASN][1000 genomes]
rs3742923	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3825742	0.85[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4474604	0.96[ASN][1000 genomes]
rs4981129	0.82[ASN][1000 genomes]
rs4981130	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4981132	0.92[ASN][1000 genomes]
rs4981133	0.92[ASN][1000 genomes]
rs4981134	0.92[ASN][1000 genomes]
rs4981135	0.92[ASN][1000 genomes]
rs4981917	0.87[ASN][1000 genomes]
rs4981918	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4981919	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4981920	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4981921	0.94[ASN][1000 genomes]
rs4981922	0.94[ASN][1000 genomes]
rs56020946	0.85[ASN][1000 genomes]
rs56208157	0.85[ASN][1000 genomes]
rs6571470	0.84[ASN][1000 genomes]
rs6571481	0.81[ASN][1000 genomes]
rs7140475	0.92[ASN][1000 genomes]
rs7141300	0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7144599	0.81[ASN][1000 genomes]
rs7148271	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7148374	0.83[ASN][1000 genomes]
rs7149538	0.81[ASN][1000 genomes]
rs7154334	0.85[ASN][1000 genomes]
rs7158089	0.80[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7161280	0.82[ASN][1000 genomes]
rs7161640	0.82[ASN][1000 genomes]
rs8003195	0.87[ASN][1000 genomes]
rs8003582	0.92[ASN][1000 genomes]
rs8005663	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs8008192	0.81[ASN][1000 genomes]
rs8013469	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8015328	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs8015523	0.84[ASN][1000 genomes]
rs8016004	0.97[ASN][1000 genomes]
rs8020037	0.82[ASN][1000 genomes]
rs8021532	0.80[ASN][1000 genomes]
rs8021918	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs8022047	0.86[ASN][1000 genomes]
rs8022995	0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs8023131	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv564180	chr14:31958566-32368934	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv564181	chr14:31958761-32363980	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv564182	chr14:32110519-32584337	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1046526	chr14:32110537-32567426	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv901593	chr14:32282564-32350371	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv526200	chr14:32308511-32454372	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2890046	ARHGAP5	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:32334000-32335200	Enhancers	Placenta	Placenta
2	chr14:32334000-32335400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr14:32334000-32335400	Enhancers	NHEK	skin
4	chr14:32334400-32334800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:32334400-32334800	Enhancers	HepG2	liver
6	chr14:32334400-32335200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr14:32334400-32335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:32334400-32335400	Enhancers	HMEC	breast

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