Variant report

Variant	rs2836946
Chromosome Location	chr21:40596763-40596764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40595422..40597101-chr21:40606197..40608970,2	K562	blood:
2	chr21:40592170..40594863-chr21:40595733..40597687,2	K562	blood:
3	chr21:40589553..40592143-chr21:40596265..40598439,3	K562	blood:
4	chr21:40590122..40592143-chr21:40596265..40598114,2	K562	blood:
5	chr21:40596378..40598646-chr21:40599484..40601519,2	K562	blood:
6	21:40595367-40598507..21:40748850-40752541	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000237373	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000229623	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1046289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11700978	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12329720	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12329767	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1554933	0.89[JPT][hapmap]
rs1888490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2142112	0.82[CHD][hapmap]
rs2178838	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2234545	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2297255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2410103	0.82[ASN][1000 genomes]
rs2776311	0.81[CHB][hapmap]
rs2836936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836990	0.89[JPT][hapmap]
rs28397992	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28460573	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28542479	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2854727	0.81[CHB][hapmap]
rs28552370	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28580194	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28590100	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28665841	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28693867	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28734946	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3761372	0.89[JPT][hapmap]
rs376720	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs379291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs383965	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs420888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs433013	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs446090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs449428	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4816613	0.82[ASN][1000 genomes]
rs4817994	0.82[ASN][1000 genomes]
rs4817995	0.85[ASN][1000 genomes]
rs4817997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4817998	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6517516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6517517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6517522	0.82[CHB][hapmap]
rs7278048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7280764	0.85[ASN][1000 genomes]
rs7281540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs741795	0.81[CHB][hapmap]
rs8126528	0.85[ASN][1000 genomes]
rs8129850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8130798	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8132993	0.81[CHB][hapmap]
rs9305665	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs9305669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9305670	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs997146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9975728	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9975909	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9975937	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9976346	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9977787	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977926	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9979691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9979936	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9981349	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9981595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9982825	0.87[EUR][1000 genomes]
rs9984518	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9984922	0.85[EUR][1000 genomes]
rs9985067	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9985148	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[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	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
2	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
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2836946	BRWD1	cis	Lymphoblastoid	GTEx
rs2836946	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs2836946	BRWD1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr21:40565400-40653600	Strong transcription	Dnd41	blood
13	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:40571400-40602400	Weak transcription	Fetal Brain Male	brain
18	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
19	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
20	chr21:40576200-40597400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr21:40577800-40598800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr21:40578000-40598800	Weak transcription	Gastric	stomach
23	chr21:40578000-40607600	Weak transcription	Aorta	Aorta
24	chr21:40578600-40608000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr21:40578800-40606600	Weak transcription	Brain Substantia Nigra	brain
26	chr21:40579000-40598800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr21:40580400-40606400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr21:40580600-40607600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr21:40580800-40607200	Weak transcription	Spleen	Spleen
30	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr21:40581800-40607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr21:40582200-40614200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr21:40582400-40597400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr21:40582400-40598600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr21:40582600-40602000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr21:40582600-40622000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr21:40583600-40606800	Weak transcription	NHLF	lung
39	chr21:40584200-40598200	Weak transcription	HepG2	liver
40	chr21:40586600-40597000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr21:40586600-40597000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr21:40586600-40599200	Weak transcription	Hela-S3	cervix
43	chr21:40587800-40598200	Weak transcription	Brain Germinal Matrix	brain
44	chr21:40587800-40599800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr21:40588000-40599600	Weak transcription	Esophagus	oesophagus
46	chr21:40588000-40601800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr21:40588600-40598600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr21:40588800-40607800	Weak transcription	Right Ventricle	heart
49	chr21:40589600-40598600	Weak transcription	Brain Anterior Caudate	brain
50	chr21:40589600-40598800	Weak transcription	Lung	lung

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