Variant report

Variant	rs9305665
Chromosome Location	chr21:40513060-40513061
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40510400..40513231-chr21:40543970..40546518,2	K562	blood:

Variant related genes	Relation type
ENSG00000235701	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1046289	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs1888490	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2297255	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2410103	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836936	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2836937	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2836941	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2836946	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2836947	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2836962	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2836963	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2836970	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2836976	0.93[CHB][hapmap]
rs2836978	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2836979	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs28552370	0.81[ASN][1000 genomes]
rs376720	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs379291	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs420888	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs446090	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4816613	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4817994	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4817995	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4817997	0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4817998	0.80[CHB][hapmap]
rs6517516	0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes]
rs6517517	0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes]
rs7278048	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs7280764	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7281540	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs8126528	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8127987	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8129850	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs9305669	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs997146	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs9979691	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs9981595	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9305665	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs9305665	BRWD1	cis	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40509400-40513600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr21:40509600-40513200	Weak transcription	Placenta	Placenta
3	chr21:40509800-40513200	Weak transcription	Fetal Muscle Leg	muscle
4	chr21:40509800-40513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:40509800-40513800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr21:40509800-40515800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr21:40510200-40513400	Weak transcription	Fetal Lung	lung
8	chr21:40510600-40515000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr21:40511600-40513400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr21:40512000-40514200	Enhancers	Fetal Thymus	thymus
11	chr21:40512800-40514200	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr21:40513000-40514000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr21:40513000-40514000	Enhancers	Thymus	Thymus

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