Variant report

Variant	rs2479757
Chromosome Location	chr13:29606913-29606914
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11618690	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11618708	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11842720	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17571410	0.88[ASN][1000 genomes]
rs17571928	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650122	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs186586	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1923519	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2475538	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2479758	0.97[ASN][1000 genomes]
rs2987336	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3011022	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs326506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs326507	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs326508	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs326520	0.96[ASN][1000 genomes]
rs4377014	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768993	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4768994	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4769659	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4769666	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56023620	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59155661	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61946436	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs621417	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.97[ASN][1000 genomes]
rs7329021	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7986484	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7992303	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994188	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7999249	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7999733	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7999783	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8000492	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8001303	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9506074	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9508229	0.96[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9508231	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9508232	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9579260	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9579264	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9783544	0.96[ASN][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	nsv533835	chr13:29141132-29962069	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2479757	SLC46A3	cis	cerebellum	SCAN
rs2479757	C13orf26	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:29585000-29609600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:29602600-29607800	Enhancers	Fetal Heart	heart
3	chr13:29606200-29623600	Weak transcription	Aorta	Aorta
4	chr13:29606600-29607600	Weak transcription	Fetal Intestine Large	intestine

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