Variant report

Variant	rs4817994
Chromosome Location	chr21:40515904-40515905
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40500620..40503419-chr21:40514957..40517352,2	MCF-7	breast:
2	chr21:40187682..40190648-chr21:40515051..40517560,2	K562	blood:
3	chr21:40515045..40517446-chr21:40522211..40524876,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1046289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11700978	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1888490	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2142112	0.82[CHD][hapmap]
rs2234545	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2297255	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2410103	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836936	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2836937	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2836941	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2836946	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs2836947	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2836962	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836963	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836970	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836976	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2836978	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836979	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2854727	0.81[CHB][hapmap]
rs28552370	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28734946	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs376720	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs379291	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs383965	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs420888	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs433013	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs446090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs449428	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4816613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4817995	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4817997	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4817998	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs6517516	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517517	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517522	0.82[CHB][hapmap]
rs7278048	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7280764	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7281540	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8126528	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8127987	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8129850	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8130798	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9305665	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9305669	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9305670	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs997146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9977787	0.82[ASN][1000 genomes]
rs9979691	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap]
rs9981595	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9984518	0.80[AMR][1000 genomes];0.85[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	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv3395554	chr21:40512728-40517052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4817994	CBR3	cis	cerebellum	SCAN
rs4817994	BRWD1	cis	multi-tissue	Pritchard
rs4817994	BRWD1	cis	cerebellum	SCAN
rs4817994	HMGN1	cis	lymphoblastoid	seeQTL
rs4817994	BRWD1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40514200-40517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:40514200-40520200	Weak transcription	Psoas Muscle	Psoas
3	chr21:40515000-40516400	Enhancers	Fetal Muscle Leg	muscle
4	chr21:40515800-40516400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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