Variant report

Variant	rs2866635
Chromosome Location	chr4:104121576-104121577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1031804	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11727498	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12501621	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17217473	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2045746	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2069274	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2126470	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2169508	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2251322	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251634	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2615539	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2623060	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2623064	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623070	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2711897	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2711898	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711899	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720448	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2720458	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2720460	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2720461	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2720462	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720464	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2720468	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2720469	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2720471	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4699050	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699051	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533056	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810571	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6813563	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815783	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6841136	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6850461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7656438	0.81[AMR][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	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830022	chr4:104087199-104257784	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2866635	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs2866635	KRT8P46	cis	lung	GTEx
rs2866635	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs2866635	BDH2	cis	Esophagus Muscularis	GTEx
rs2866635	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs2866635	BDH2	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104120200-104122800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:104120400-104122000	Weak transcription	Fetal Intestine Large	intestine
3	chr4:104120400-104122800	Enhancers	HepG2	liver
4	chr4:104121000-104122000	Weak transcription	Fetal Intestine Small	intestine

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