Variant report

Variant	rs2103654
Chromosome Location	chr20:41333138-41333139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1040481	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11086848	0.88[EUR][1000 genomes]
rs12479621	0.96[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs12624619	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13038370	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs13042288	0.82[EUR][1000 genomes]
rs13043908	0.88[EUR][1000 genomes]
rs16987210	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2017914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206428	0.96[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2206431	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2425515	0.92[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2425520	0.96[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2425536	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2425537	0.81[CEU][hapmap]
rs2867491	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2867493	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2867494	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs3091578	0.84[EUR][1000 genomes]
rs3092078	0.84[EUR][1000 genomes]
rs3092270	0.81[EUR][1000 genomes]
rs3092592	0.96[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs34079161	0.84[EUR][1000 genomes]
rs36020805	0.83[EUR][1000 genomes]
rs4810363	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4810364	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4810365	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4810366	0.96[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs4810367	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4812621	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4812622	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4812623	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4812624	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4812625	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4812626	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4812628	0.85[EUR][1000 genomes]
rs4812629	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4812630	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs4812631	0.96[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs4812632	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs55796409	0.88[EUR][1000 genomes]
rs6065525	0.96[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs6065527	0.88[EUR][1000 genomes]
rs6072817	0.83[EUR][1000 genomes]
rs6072823	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6072824	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6072826	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6072833	0.96[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs73112427	0.86[EUR][1000 genomes]
rs742420	0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs926482	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064253	chr20:41120425-41379706	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	nsv532517	chr20:41188651-41342196	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv949644	chr20:41207365-41333541	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv912878	chr20:41222480-41361424	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv833988	chr20:41227788-41379921	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv586028	chr20:41296994-41381215	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1060878	chr20:41317182-41342290	Weak transcription Strong transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2103654	LOC79015	cis	parietal	SCAN
rs2103654	PKIG	cis	parietal	SCAN
rs2103654	WFDC3	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41330000-41335200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr20:41330000-41335400	Weak transcription	Colon Smooth Muscle	Colon
3	chr20:41330400-41335400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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