Variant report

Variant	rs9984518
Chromosome Location	chr21:40583166-40583167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40569031..40571999-chr21:40581201..40583406,2	K562	blood:
2	chr21:40582888..40584633-chr21:40585013..40587494,2	MCF-7	breast:
3	chr21:40556483..40559803-chr21:40580058..40583280,3	K562	blood:
4	21:40581316-40583765..21:40748850-40752541	GM12878	blood:
5	21:40581316-40583765..21:40757151-40764378	GM12878	blood:
6	chr21:40581211..40583569-chr21:40670765..40672444,2	K562	blood:
7	chr21:40572247..40574519-chr21:40580812..40583327,2	K562	blood:
8	chr21:40574761..40577366-chr21:40579952..40583653,3	MCF-7	breast:
9	chr21:40574695..40577813-chr21:40579621..40584653,4	K562	blood:
10	chr21:40582005..40584488-chr8:97183248..97185340,2	MCF-7	breast:
11	21:40581316-40583765..21:40809171-40812812	GM12878	blood:
12	chr21:40581504..40583471-chr21:40586108..40588816,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000227406	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000232608	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000157578	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1046289	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11700978	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12329720	0.81[ASN][1000 genomes]
rs12329767	0.81[ASN][1000 genomes]
rs2178838	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2234545	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297255	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2410103	0.85[ASN][1000 genomes]
rs2836936	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836937	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836941	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836946	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836947	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836962	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836963	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836970	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836976	0.85[ASN][1000 genomes]
rs2836978	0.86[ASN][1000 genomes]
rs2836979	0.86[ASN][1000 genomes]
rs28397992	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28460573	0.81[ASN][1000 genomes]
rs28542479	0.86[ASN][1000 genomes]
rs28552370	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28580194	0.81[ASN][1000 genomes]
rs28590100	0.81[ASN][1000 genomes]
rs28665841	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28693867	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28734946	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376720	0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs379291	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs383965	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs420888	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs433013	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs446090	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs449428	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4816613	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4817994	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4817995	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4817997	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6517516	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6517517	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7278048	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7280764	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7281540	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8126528	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8129850	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8130798	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9305669	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9305670	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9975728	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9975909	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9975937	0.81[ASN][1000 genomes]
rs9976346	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9977787	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9977926	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9979691	0.84[ASN][1000 genomes]
rs9979936	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9981349	0.81[ASN][1000 genomes]
rs9981595	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9985148	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9984518	BRWD1	cis	multi-tissue	Pritchard
rs9984518	BRWD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
3	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40563600-40588600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr21:40564800-40587800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:40565000-40592600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr21:40565400-40653600	Strong transcription	Dnd41	blood
16	chr21:40565600-40585600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr21:40565600-40590200	Strong transcription	Liver	Liver
18	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr21:40565800-40590600	Strong transcription	Fetal Thymus	thymus
20	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr21:40566200-40590600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr21:40566200-40590600	Strong transcription	Adipose Nuclei	Adipose
23	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:40567400-40585400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr21:40567400-40592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr21:40567600-40583800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr21:40567600-40585000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr21:40568200-40584600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr21:40570600-40589800	Weak transcription	Stomach Mucosa	stomach
31	chr21:40571400-40602400	Weak transcription	Fetal Brain Male	brain
32	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
33	chr21:40573400-40583600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr21:40573400-40583600	Strong transcription	NHDF-Ad	bronchial
35	chr21:40573800-40593600	Weak transcription	A549	lung
36	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
37	chr21:40575200-40589400	Weak transcription	NHEK	skin
38	chr21:40576200-40590400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr21:40576200-40597400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr21:40576400-40592400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr21:40576600-40584200	Strong transcription	HepG2	liver
42	chr21:40576600-40588600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr21:40576600-40589000	Strong transcription	Primary B cells from cord blood	blood
44	chr21:40576800-40589600	Weak transcription	HUVEC	blood vessel
45	chr21:40576800-40593600	Weak transcription	Right Atrium	heart
46	chr21:40577000-40586600	Strong transcription	HSMM	muscle
47	chr21:40577200-40593800	Weak transcription	Colon Smooth Muscle	Colon
48	chr21:40577200-40595400	Weak transcription	Colonic Mucosa	Colon
49	chr21:40577600-40586800	Weak transcription	Esophagus	oesophagus
50	chr21:40577600-40587000	Weak transcription	Brain Angular Gyrus	brain

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