Variant report

Variant	rs12109973
Chromosome Location	chr5:167272333-167272334
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1024970	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12189098	0.91[CEU][hapmap]
rs12522225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12716236	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13165876	0.88[ASN][1000 genomes]
rs13182072	0.91[CEU][hapmap]
rs1363205	0.91[CEU][hapmap]
rs1421979	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1421982	0.91[CEU][hapmap]
rs1421983	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1963355	0.80[EUR][1000 genomes]
rs2112309	0.82[EUR][1000 genomes]
rs4632816	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs6555773	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6555775	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7719650	0.85[CEU][hapmap]
rs7729681	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	nsv932627	chr5:166744408-167290959	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1027805	chr5:167082800-167285008	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12109973	ST20	trans	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167251800-167299000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:167252600-167276000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:167266600-167326200	Weak transcription	HMEC	breast
4	chr5:167266800-167272800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:167267800-167272800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:167269000-167278000	Strong transcription	NHEK	skin
7	chr5:167270400-167272400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:167271200-167280000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:167271600-167276000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:167271800-167276200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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