Variant report

Variant	rs28580194
Chromosome Location	chr21:40682773-40682774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40682558-40682857	K562	blood:	n/a	n/a
2	POLR2A	chr21:40682548-40682855	K562	blood:	n/a	n/a
3	POLR2A	chr21:40682578-40684658	K562	blood:	n/a	n/a
4	POLR2A	chr21:40682624-40682781	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40672762..40675001-chr21:40682440..40684098,2	K562	blood:
2	chr21:40645807..40648656-chr21:40680491..40682941,2	K562	blood:
3	chr21:40682124..40685118-chr21:40763752..40765296,2	K562	blood:
4	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
5	chr21:40645055..40648656-chr21:40680491..40684092,3	K562	blood:
6	chr21:40681416..40687854-chr21:40744378..40751195,8	K562	blood:
7	chr21:40554270..40557456-chr21:40682408..40685088,3	K562	blood:
8	chr21:40591760..40593585-chr21:40682186..40684474,2	K562	blood:
9	chr21:40668014..40669940-chr21:40681557..40684495,2	K562	blood:

No data

Variant related genes	Relation type
BRWD1-AS1	TF binding region
ENSG00000252915	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000205581	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10154073	0.84[EUR][1000 genomes]
rs12329720	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12329767	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070866	0.83[EUR][1000 genomes]
rs2178838	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2234545	0.81[EUR][1000 genomes]
rs2836941	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836946	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836947	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836962	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836963	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836970	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836976	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836978	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836979	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28397992	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28460573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494168	0.87[EUR][1000 genomes]
rs28542479	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28590100	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665841	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28684434	0.87[EUR][1000 genomes]
rs28693867	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28734946	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818020	0.84[EUR][1000 genomes]
rs4818026	0.84[EUR][1000 genomes]
rs7278048	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8130083	0.83[EUR][1000 genomes]
rs9284464	0.84[EUR][1000 genomes]
rs9305673	0.83[EUR][1000 genomes]
rs997146	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9974266	0.83[EUR][1000 genomes]
rs9975256	0.87[EUR][1000 genomes]
rs9975728	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9975909	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9975937	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9976346	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9977787	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9977926	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9979571	0.84[EUR][1000 genomes]
rs9979691	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979936	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9981349	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981527	0.83[EUR][1000 genomes]
rs9982825	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9982870	0.84[EUR][1000 genomes]
rs9984518	0.81[ASN][1000 genomes]
rs9984922	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9985067	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9985148	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][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	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3429298	chr21:40670131-40688774	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28580194	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs28580194	BRWD1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
2	chr21:40643800-40684200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40646600-40683400	Weak transcription	Fetal Brain Male	brain
4	chr21:40655000-40683000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr21:40655400-40683200	Strong transcription	Dnd41	blood
6	chr21:40656400-40683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:40661800-40683400	Weak transcription	Stomach Mucosa	stomach
8	chr21:40663600-40683400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr21:40664000-40684200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr21:40665000-40683800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr21:40665200-40684400	Weak transcription	Colonic Mucosa	Colon
12	chr21:40667000-40684000	Weak transcription	HSMMtube	muscle
13	chr21:40667000-40684200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr21:40669200-40684200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr21:40669400-40684000	Weak transcription	HUVEC	blood vessel
16	chr21:40669400-40684400	Weak transcription	Esophagus	oesophagus
17	chr21:40669800-40683800	Weak transcription	Brain Substantia Nigra	brain
18	chr21:40670400-40683800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr21:40670600-40683200	Weak transcription	NHDF-Ad	bronchial
20	chr21:40671400-40683200	Weak transcription	HMEC	breast
21	chr21:40672200-40684000	Weak transcription	Aorta	Aorta
22	chr21:40672400-40683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr21:40672400-40684000	Weak transcription	Small Intestine	intestine
24	chr21:40672600-40683800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr21:40672600-40684400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr21:40672800-40683400	Weak transcription	Fetal Heart	heart
27	chr21:40672800-40683800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr21:40673600-40683200	Weak transcription	Primary B cells from cord blood	blood
29	chr21:40673600-40683400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr21:40673600-40683600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr21:40673600-40683600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr21:40673600-40683600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr21:40673600-40683800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr21:40673600-40684000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr21:40673600-40684400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr21:40673600-40684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr21:40673800-40683800	Weak transcription	Fetal Kidney	kidney
38	chr21:40675000-40683800	Weak transcription	A549	lung
39	chr21:40675400-40683400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr21:40675800-40683400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr21:40675800-40683800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr21:40675800-40684200	Weak transcription	Pancreas	Pancrea
43	chr21:40675800-40684400	Weak transcription	Gastric	stomach
44	chr21:40675800-40684400	Weak transcription	Spleen	Spleen
45	chr21:40676400-40683600	Weak transcription	Colon Smooth Muscle	Colon
46	chr21:40676600-40683800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr21:40676600-40684000	Weak transcription	Brain Germinal Matrix	brain
48	chr21:40676800-40683400	Weak transcription	Adipose Nuclei	Adipose
49	chr21:40676800-40683600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr21:40676800-40683800	Weak transcription	GM12878-XiMat	blood

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