Variant report

Variant	rs12362590
Chromosome Location	chr11:64352540-64352541
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64350444..64353414-chr11:64386038..64388659,2	MCF-7	breast:
2	chr11:64323432..64325391-chr11:64351236..64353955,2	K562	blood:
3	chr11:64350498..64353447-chr11:64359000..64361623,2	MCF-7	breast:
4	11:64349180-64353532..11:64523887-64530985	Hela-S3	cervix:
5	11:64349180-64353532..11:64402707-64415880	Hela-S3	cervix:
6	11:64349180-64353532..11:64415880-64426617	K562	blood:
7	11:64349180-64353532..11:64489786-64499245	K562	blood:
8	11:64349180-64353532..11:64501239-64517861	K562	blood:

Variant related genes	Relation type
ENSG00000110076	Chromatin interaction
ENSG00000168065	Chromatin interaction
ENSG00000237410	Chromatin interaction
ENSG00000068831	Chromatin interaction
ENSG00000068976	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10792441	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10792443	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10897518	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11231825	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11231845	0.85[EUR][1000 genomes]
rs11602903	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11606370	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11607663	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12365089	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12786214	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12802649	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1529909	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2021860	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2277311	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2360872	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2360873	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2666559	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35195142	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3825016	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3825018	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs475642	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs492175	0.82[EUR][1000 genomes]
rs4930556	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs505802	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs506338	0.82[EUR][1000 genomes]
rs524023	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs526338	0.84[EUR][1000 genomes]
rs528211	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs531763	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs537246	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs538737	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs544838	0.81[EUR][1000 genomes]
rs552307	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs555456	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs559946	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs561193	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7102344	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7932437	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs80841	0.82[EUR][1000 genomes]
rs893006	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs893007	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9734313	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035485	chr11:64228847-64354869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897692	chr11:64305452-64386526	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
3	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
9	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
10	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12362590	NRXN2	cis	lung	GTEx
rs12362590	SF1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64352200-64352600	Weak transcription	HepG2	liver
2	chr11:64352200-64353800	Weak transcription	Spleen	Spleen
3	chr11:64352200-64356800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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