Variant report

Variant	rs11024460
Chromosome Location	chr11:18084182-18084183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18034389..18036116-chr11:18083938..18086821,2	MCF-7	breast:
2	chr11:18083345..18085878-chr11:18088816..18091112,3	K562	blood:

Variant related genes	Relation type
ENSG00000129158	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10500831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10832871	0.83[CHD][hapmap];0.83[MEX][hapmap]
rs10832876	0.83[MEX][hapmap]
rs10832880	0.99[EUR][1000 genomes]
rs10832882	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11024433	0.83[CHD][hapmap];0.83[MEX][hapmap]
rs11024449	0.83[CEU][hapmap];0.83[MEX][hapmap]
rs11024458	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11024461	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11024468	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11024476	0.94[EUR][1000 genomes]
rs11024482	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11024484	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11024485	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11024493	0.83[EUR][1000 genomes]
rs12363226	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12364327	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12792460	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs172423	0.83[MEX][hapmap]
rs1975777	0.83[CEU][hapmap]
rs211105	0.83[MEX][hapmap]
rs2468842	0.81[CEU][hapmap]
rs35447333	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4052539	0.83[CEU][hapmap]
rs5790015	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61882530	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6486406	0.81[CEU][hapmap]
rs7117439	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7118373	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7131255	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7131454	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7929920	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933259	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7934091	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7942794	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7943725	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7943884	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11024460	SAAL1	cis	Artery Tibial	GTEx
rs11024460	SAAL1	cis	parietal	SCAN
rs11024460	SAAL1	cis	Esophagus Muscularis	GTEx
rs11024460	SAAL1	trans	brain	seeQTL
rs11024460	SAAL1	cis	cerebellum	SCAN
rs11024460	SAAL1	cis	brain	seeQTL
rs11024460	MRGPRX3	cis	lesional skin	skin_eQTL
rs11024460	SAAL1	cis	lymphoblastoid	seeQTL
rs11024460	SAAL1	cis	multi-tissue	Pritchard
rs11024460	SAAL1	cis	Skin Sun Exposed Lower leg	GTEx
rs11024460	SAAL1	cis	lung	GTEx
rs11024460	TPH1	cis	cerebellum	SCAN
rs11024460	SAAL1	cis	Adipose Subcutaneous	GTEx
rs11024460	MRGPRX3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18070800-18102600	Weak transcription	Brain Hippocampus Middle	brain
2	chr11:18081400-18100400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr11:18083200-18109000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr11:18083400-18102400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:18083800-18084800	Weak transcription	Liver	Liver

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