Variant report

Variant	rs2836962
Chromosome Location	chr21:40628982-40628983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40628735..40630944-chr21:40634628..40637313,2	MCF-7	breast:
2	chr21:40628747..40631988-chr21:40636512..40639604,3	K562	blood:

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1046289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11700978	0.81[EUR][1000 genomes]
rs12329720	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12329767	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1554933	0.89[JPT][hapmap]
rs1888490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2178838	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234545	0.90[EUR][1000 genomes]
rs2297255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2776311	0.82[CHB][hapmap]
rs2836936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2836937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2836941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28460573	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28542479	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2854727	0.81[CHB][hapmap]
rs28552370	0.84[EUR][1000 genomes]
rs28580194	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28590100	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28665841	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28693867	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734946	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3761372	0.89[JPT][hapmap]
rs376720	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs379291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs420888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs433013	0.81[EUR][1000 genomes]
rs446090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs449428	0.81[EUR][1000 genomes]
rs4817997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4817998	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6517516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6517517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6517522	0.82[CHB][hapmap]
rs7278048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7281540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs741795	0.82[CHB][hapmap]
rs8129850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8130798	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8132993	0.81[CHB][hapmap]
rs9305665	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs9305669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9305670	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs997146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9975728	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975909	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9975937	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9976346	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977787	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9977926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979936	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981349	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9981595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9982825	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9984518	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9984922	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9985067	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9985148	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2836962	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs2836962	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	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
2	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr21:40565400-40653600	Strong transcription	Dnd41	blood
9	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
11	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
12	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr21:40593400-40650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr21:40597200-40635600	Weak transcription	Fetal Heart	heart
16	chr21:40598200-40629800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr21:40603200-40653400	Weak transcription	Right Atrium	heart
18	chr21:40608400-40632200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr21:40608400-40632600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr21:40608400-40634200	Weak transcription	NHLF	lung
21	chr21:40608400-40638200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr21:40608600-40636400	Weak transcription	Aorta	Aorta
24	chr21:40609800-40635400	Weak transcription	Fetal Brain Male	brain
25	chr21:40613400-40652000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr21:40613800-40651000	Strong transcription	Fetal Thymus	thymus
27	chr21:40614000-40654400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr21:40614600-40654200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr21:40614800-40635000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr21:40614800-40652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr21:40615800-40639800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr21:40616400-40630600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr21:40616400-40631000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr21:40616400-40651800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr21:40616600-40631400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr21:40617400-40635200	Weak transcription	Colonic Mucosa	Colon
37	chr21:40618000-40632200	Weak transcription	NHEK	skin
38	chr21:40618000-40659200	Weak transcription	Stomach Mucosa	stomach
39	chr21:40618400-40635400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr21:40619000-40638000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr21:40619400-40656200	Weak transcription	Ovary	ovary
42	chr21:40619600-40635800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr21:40619600-40660200	Weak transcription	Brain Angular Gyrus	brain
44	chr21:40619800-40629600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr21:40620000-40635200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr21:40620000-40640400	Weak transcription	A549	lung
47	chr21:40620200-40636800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr21:40620400-40635400	Weak transcription	HUVEC	blood vessel
49	chr21:40620800-40636800	Weak transcription	Spleen	Spleen
50	chr21:40621600-40630000	Weak transcription	Placenta Amnion	Placenta Amnion

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