Variant report

Variant	rs10496040
Chromosome Location	chr2:55307646-55307647
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55306855..55308642-chr2:55313983..55316213,2	K562	blood:
2	chr2:55306577..55308531-chr2:55314255..55316855,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf63-2	chr2:55307625-55307775	NONHSAT070760

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1012603	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10496034	0.80[EUR][1000 genomes]
rs11683784	0.80[GIH][hapmap]
rs11884082	0.88[AFR][1000 genomes]
rs11887323	1.00[CHB][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11899295	0.94[LWK][hapmap]
rs17046514	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs17046545	0.89[LWK][hapmap]
rs17046583	0.82[CEU][hapmap]
rs17046643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17046658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241958	0.90[EUR][1000 genomes]
rs4233955	0.80[EUR][1000 genomes]
rs4671993	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs4671995	0.80[EUR][1000 genomes]
rs4671997	0.80[EUR][1000 genomes]
rs4672006	0.80[EUR][1000 genomes]
rs4672009	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4672011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57737203	0.84[EUR][1000 genomes]
rs58156158	0.91[AFR][1000 genomes]
rs60553807	0.86[EUR][1000 genomes]
rs60989687	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724138	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs73936818	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73936821	0.83[AFR][1000 genomes]
rs73936824	0.85[AFR][1000 genomes]
rs73936829	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs957920	0.88[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10496040	RTN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55299200-55318000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:55304400-55309200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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