Variant report

Variant	rs4671233
Chromosome Location	chr2:55151440-55151441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55150702..55153122-chr2:55154482..55158457,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10179594	0.82[CEU][hapmap]
rs10196667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs10205017	0.84[EUR][1000 genomes]
rs10746530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs11125551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11904457	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12475185	0.97[ASN][1000 genomes]
rs12989576	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[EUR][1000 genomes]
rs13002841	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs13008105	0.97[ASN][1000 genomes]
rs13020490	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13023202	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13026576	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13028800	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17417648	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs17418111	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2116491	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2304685	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2580766	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2588520	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2919125	1.00[CEU][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2920863	0.82[CEU][hapmap]
rs2920883	0.82[CEU][hapmap]
rs2920884	0.82[CEU][hapmap]
rs2920897	0.82[CEU][hapmap]
rs2968789	0.82[CEU][hapmap]
rs34227740	1.00[AFR][1000 genomes]
rs34564860	1.00[AFR][1000 genomes]
rs36024305	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs36063689	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4233956	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4504034	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4525735	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4671998	0.94[ASN][1000 genomes]
rs55777421	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6545462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs67721747	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7559248	1.00[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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4671233	RTN4	cis	Thyroid	GTEx
rs4671233	SPTBN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55134000-55153800	Weak transcription	Brain Angular Gyrus	brain
2	chr2:55134400-55153600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:55148600-55155600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:55150000-55168400	Weak transcription	Pancreas	Pancrea

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