Variant report

Variant	rs401843
Chromosome Location	chr2:21524976-21524977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10185261	0.83[EUR][1000 genomes]
rs10185535	0.83[EUR][1000 genomes]
rs10192339	0.83[EUR][1000 genomes]
rs10196906	0.83[EUR][1000 genomes]
rs10199484	0.83[EUR][1000 genomes]
rs10199765	0.83[EUR][1000 genomes]
rs12467767	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs21730	0.84[EUR][1000 genomes]
rs219505	0.83[EUR][1000 genomes]
rs219506	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219507	0.83[EUR][1000 genomes]
rs219508	0.83[EUR][1000 genomes]
rs219509	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219510	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219531	0.83[EUR][1000 genomes]
rs219532	0.84[EUR][1000 genomes]
rs219533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs219534	0.84[EUR][1000 genomes]
rs219535	0.84[EUR][1000 genomes]
rs219536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs219537	0.84[EUR][1000 genomes]
rs219538	0.84[EUR][1000 genomes]
rs219539	0.82[EUR][1000 genomes]
rs219540	0.84[EUR][1000 genomes]
rs219541	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs219546	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2217745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380969	0.84[EUR][1000 genomes]
rs389795	0.84[EUR][1000 genomes]
rs390062	0.84[EUR][1000 genomes]
rs391070	0.84[EUR][1000 genomes]
rs399991	0.83[EUR][1000 genomes]
rs412558	0.84[EUR][1000 genomes]
rs418451	0.84[EUR][1000 genomes]
rs423277	0.84[EUR][1000 genomes]
rs425440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439907	0.84[EUR][1000 genomes]
rs55815563	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55841071	0.84[EUR][1000 genomes]
rs56286635	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59020225	0.84[EUR][1000 genomes]
rs59920883	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61603728	0.83[EUR][1000 genomes]
rs6704721	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6708193	0.81[ASN][1000 genomes]
rs72789650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72789652	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72789656	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7369047	0.83[EUR][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	nsv1011486	chr2:21475803-22364002	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535602	chr2:21475803-22364002	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1003630	chr2:21521637-21546859	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs401843	GEN1	cis	cerebellum	SCAN
rs401843	RHOB	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:21511400-21527400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:21513000-21538200	Weak transcription	Aorta	Aorta
3	chr2:21524800-21526200	Enhancers	Fetal Brain Male	brain

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