Variant report

Variant	rs6030218
Chromosome Location	chr20:41053747-41053748
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1125550	0.88[ASN][1000 genomes]
rs2179217	0.87[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2205945	0.87[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs2425497	0.86[CHB][hapmap]
rs2425498	0.82[CHB][hapmap]
rs4810356	0.81[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs4812598	0.87[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs4812599	0.90[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4812600	0.95[ASN][1000 genomes]
rs6016785	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs6016791	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6016792	0.90[ASN][1000 genomes]
rs6030212	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6030215	0.92[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs6030216	0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6030217	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6030224	0.87[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs6030226	0.90[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6030229	0.81[CHB][hapmap]
rs6030232	0.87[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs6030233	0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs6102826	0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6513791	0.87[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs7268459	0.87[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs8123429	0.93[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs978456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6030218	JPH2	cis	cerebellum	SCAN
rs6030218	DBNDD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41042000-41070000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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