Variant report

Variant	rs12492380
Chromosome Location	chr3:133597103-133597104
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133592957..133596449-chr3:133596615..133599487,3	MCF-7	breast:
2	chr3:133590405..133593103-chr3:133594407..133597314,2	K562	blood:
3	chr3:133595806..133598075-chr3:133598374..133600907,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10212397	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935088	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs11706007	0.87[ASN][1000 genomes]
rs13325953	0.87[ASN][1000 genomes]
rs1589900	0.87[ASN][1000 genomes]
rs1880667	0.86[JPT][hapmap]
rs1917781	0.86[JPT][hapmap]
rs2222633	0.87[ASN][1000 genomes]
rs2222634	0.87[ASN][1000 genomes]
rs2370639	0.87[ASN][1000 genomes]
rs3811663	0.88[ASN][1000 genomes]
rs6762758	0.82[ASN][1000 genomes]
rs6787108	0.82[ASN][1000 genomes]
rs7636726	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs7638839	0.87[ASN][1000 genomes]
rs7641276	0.87[ASN][1000 genomes]
rs7651963	0.87[ASN][1000 genomes]
rs940898	0.86[JPT][hapmap]
rs9813363	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9815710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819520	0.90[MEX][hapmap]
rs9824250	0.84[ASN][1000 genomes]
rs9824788	0.85[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs9840311	0.82[ASN][1000 genomes]
rs9844944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9852801	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9861470	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879849	0.82[ASN][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	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12492380	RYK	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133590600-133606600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:133591400-133598200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:133592000-133602000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:133592400-133598400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:133592400-133602800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:133592400-133605800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:133596200-133600000	Weak transcription	K562	blood
8	chr3:133596400-133613600	Weak transcription	Gastric	stomach
9	chr3:133596600-133598000	Weak transcription	Left Ventricle	heart

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