Variant report

Variant	rs12792460
Chromosome Location	chr11:18076439-18076440
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18070729..18072614-chr11:18074865..18077742,2	K562	blood:
2	chr11:18033001..18035448-chr11:18075217..18077710,2	K562	blood:

Variant related genes	Relation type
ENSG00000129158	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10500831	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10832880	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10832882	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024458	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024460	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11024461	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024468	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024476	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024482	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024484	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024485	0.85[EUR][1000 genomes]
rs11024493	0.83[ASN][1000 genomes]
rs12363226	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12364327	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2168361	0.81[ASN][1000 genomes]
rs2263407	0.81[ASN][1000 genomes]
rs2468841	0.81[ASN][1000 genomes]
rs2468842	0.81[ASN][1000 genomes]
rs35447333	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052539	0.81[ASN][1000 genomes]
rs5790015	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61882530	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7117439	0.85[EUR][1000 genomes]
rs7118373	0.85[EUR][1000 genomes]
rs7131255	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7131454	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7929920	0.89[EUR][1000 genomes]
rs7933259	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7934091	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7942794	0.85[EUR][1000 genomes]
rs7943725	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7943884	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907923	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3347952	chr11:18074651-18077199	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3346247	chr11:18074801-18077349	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3438822	chr11:18075026-18076774	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12792460	SERGEF	cis	Adipose Subcutaneous	GTEx
rs12792460	SAAL1	cis	Artery Tibial	GTEx
rs12792460	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs12792460	RP1-59M18.2	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18070800-18102600	Weak transcription	Brain Hippocampus Middle	brain
2	chr11:18072200-18076600	Weak transcription	Gastric	stomach
3	chr11:18076200-18077000	Enhancers	Stomach Mucosa	stomach
4	chr11:18076400-18077600	Enhancers	Aorta	Aorta

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