Variant report

Variant	rs6030229
Chromosome Location	chr20:41059393-41059394
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1125550	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11700137	0.88[CHD][hapmap]
rs2049971	0.84[ASN][1000 genomes]
rs2142795	0.93[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2179217	0.93[CHB][hapmap];0.83[AMR][1000 genomes]
rs2205945	0.93[CEU][hapmap];0.93[CHB][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.90[AMR][1000 genomes]
rs2425492	0.88[ASN][1000 genomes]
rs2425494	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2425496	0.86[AMR][1000 genomes]
rs2425497	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2425498	0.88[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4810356	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4812598	0.86[CEU][hapmap];0.93[CHB][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4812600	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6016785	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6016791	0.97[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs6016792	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6030212	0.89[ASN][1000 genomes]
rs6030215	0.90[CEU][hapmap];0.92[CHB][hapmap];0.83[AMR][1000 genomes]
rs6030216	0.86[CEU][hapmap];0.93[CHB][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6030217	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6030218	0.81[CHB][hapmap]
rs6030224	0.93[CEU][hapmap];0.93[CHB][hapmap];0.90[AMR][1000 genomes]
rs6030232	0.86[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs6030233	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs6030236	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6030238	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6030239	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6072745	0.86[AMR][1000 genomes]
rs6102826	0.85[CEU][hapmap];0.93[CHB][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6513791	1.00[CEU][hapmap];0.93[CHB][hapmap];0.80[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7268459	0.93[CEU][hapmap];0.93[CHB][hapmap];0.90[AMR][1000 genomes]
rs8123429	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs932320	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs978457	0.81[CHB][hapmap]

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	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv833987	chr20:41007663-41184914	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6030229	AMACR	trans	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41042000-41070000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:41058000-41060000	Enhancers	Adipose Nuclei	Adipose
3	chr20:41058200-41059400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr20:41058800-41059600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:41059200-41061000	Weak transcription	Fetal Muscle Leg	muscle

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