Variant report

Variant	rs6030469
Chromosome Location	chr20:41412460-41412461
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10485697	0.88[CEU][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs11696719	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes]
rs11698606	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11698607	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11698772	0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11699773	0.88[CEU][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs1535237	0.88[CEU][hapmap]
rs16987367	0.90[AMR][1000 genomes]
rs16987425	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs17811425	0.82[YRI][hapmap]
rs2015675	0.80[AMR][1000 genomes]
rs6016891	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6030467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7261303	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs7265982	0.80[GIH][hapmap]
rs7268984	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs7273962	0.91[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915994	chr20:41180550-41464507	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1058990	chr20:41289969-41543912	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv544277	chr20:41289969-41543912	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6030469	WFDC12	cis	parietal	SCAN
rs6030469	R3HDML	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41407400-41420800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr20:41409600-41413800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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Input of quick search could be:

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

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