Variant report

Variant	rs2972072
Chromosome Location	chr2:55295370-55295371
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55293555..55295689-chr2:55296862..55299716,2	K562	blood:
2	chr2:55288774..55290302-chr2:55293407..55295597,2	K562	blood:
3	chr2:55276234..55278687-chr2:55294375..55296735,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10174838	0.83[EUR][1000 genomes]
rs10210840	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11674808	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713284	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs13011689	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13387751	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2044291	0.86[EUR][1000 genomes]
rs2255112	0.82[TSI][hapmap]
rs2580765	0.82[TSI][hapmap]
rs2580772	0.92[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2580776	0.82[EUR][1000 genomes]
rs2588510	0.82[TSI][hapmap]
rs2588518	0.81[CEU][hapmap]
rs2860453	0.88[CEU][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs2919129	0.88[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2920862	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2920878	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920893	0.87[EUR][1000 genomes]
rs2920900	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968786	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2968790	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968793	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968794	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968795	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968798	0.86[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs2968822	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968825	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968827	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972070	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972071	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972075	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972097	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs35631428	0.83[EUR][1000 genomes]
rs4672005	0.85[EUR][1000 genomes]
rs6545466	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6726158	0.83[EUR][1000 genomes]
rs6755468	0.92[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs6760429	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7340476	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7562292	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7570629	0.88[CEU][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2972072	RTN4	cis	Artery Aorta	GTEx
rs2972072	RTN4	cis	Artery Tibial	GTEx
rs2972072	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs2972072	RTN4	cis	Nerve Tibial	GTEx
rs2972072	RTN4	cis	Adipose Subcutaneous	GTEx
rs2972072	RTN4	cis	Thyroid	GTEx
rs2972072	RTN4	cis	Esophagus Mucosa	GTEx
rs2972072	RTN4	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55293000-55295400	Weak transcription	Fetal Heart	heart
2	chr2:55293000-55298400	Weak transcription	K562	blood

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