Variant report

Variant	rs6016798
Chromosome Location	chr20:41075396-41075397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11697017	0.89[CEU][hapmap]
rs2076081	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2076082	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58338621	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6016797	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs6016801	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6016803	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs6030245	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs6030251	0.89[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6030252	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6030253	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6065482	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6072747	0.83[JPT][hapmap]
rs6130136	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6130137	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[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
rs6016798	C20orf111	cis	cerebellum	SCAN
rs6016798	WFDC10B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41070000-41077800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:41072000-41078200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr20:41072600-41078600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr20:41074200-41075400	Weak transcription	Adipose Nuclei	Adipose
5	chr20:41075200-41075800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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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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