Variant report

Variant	rs6048326
Chromosome Location	chr20:22731513-22731514
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11087395	0.81[EUR][1000 genomes]
rs11907108	0.80[EUR][1000 genomes]
rs12479587	0.81[EUR][1000 genomes]
rs13036614	0.83[EUR][1000 genomes]
rs13036740	0.83[EUR][1000 genomes]
rs13037649	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13037976	0.83[EUR][1000 genomes]
rs4371419	0.80[EUR][1000 genomes]
rs4514951	0.80[EUR][1000 genomes]
rs4603850	0.80[EUR][1000 genomes]
rs6036200	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6036203	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036204	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036205	0.83[EUR][1000 genomes]
rs6036206	0.83[EUR][1000 genomes]
rs6036212	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6036213	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6048280	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048283	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048284	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048291	0.80[EUR][1000 genomes]
rs6048298	0.80[EUR][1000 genomes]
rs6048300	0.83[CEU][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs6048302	0.87[TSI][hapmap]
rs6048327	0.83[EUR][1000 genomes]
rs6048331	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6048332	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6048333	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6075943	0.83[EUR][1000 genomes]
rs7262725	0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs7270196	0.80[EUR][1000 genomes]
rs7270365	0.80[EUR][1000 genomes]
rs7270374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs965762	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061382	chr20:22706041-22763200	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1057305	chr20:22711334-22733613	ZNF genes & repeats Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv544213	chr20:22722740-22791150	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6048326	GGTLC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22726000-22739000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:22731400-22732800	Enhancers	Placenta	Placenta

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