Variant report

Variant	rs6030407
Chromosome Location	chr20:41308546-41308547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11905283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16987202	0.98[EUR][1000 genomes]
rs16987229	1.00[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs16987276	1.00[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs2206430	0.96[EUR][1000 genomes]
rs4140493	0.98[EUR][1000 genomes]
rs4560192	0.98[EUR][1000 genomes]
rs4810370	1.00[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4812615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4812617	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4812618	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4812633	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4812635	0.87[EUR][1000 genomes]
rs4812637	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4812638	0.89[EUR][1000 genomes]
rs59581792	0.90[EUR][1000 genomes]
rs6030404	0.98[EUR][1000 genomes]
rs6030405	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6030409	0.98[EUR][1000 genomes]
rs6030410	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs6030432	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6030433	1.00[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6030434	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6030435	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs60886646	0.92[EUR][1000 genomes]
rs6093718	0.94[EUR][1000 genomes]
rs6093719	0.92[EUR][1000 genomes]
rs6102978	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6102979	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6102986	0.98[EUR][1000 genomes]
rs6102987	1.00[CEU][hapmap]
rs6102990	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6102993	0.92[EUR][1000 genomes]
rs6102994	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6102995	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6102997	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6103000	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6103005	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6103008	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6103012	0.81[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7362290	0.98[EUR][1000 genomes]
rs742419	0.89[EUR][1000 genomes]
rs8115740	0.98[EUR][1000 genomes]
rs8120378	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs926480	0.86[TSI][hapmap]
rs970283	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs976248	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs976249	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41304000-41309600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:41306600-41313000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr20:41306800-41310200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:41306800-41311000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr20:41306800-41314000	Weak transcription	Pancreas	Pancrea

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