Variant report

Variant	rs449428
Chromosome Location	chr21:40542633-40542634
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	chr21:40539973..40543967-chr21:40547698..40550109,4	MCF-7	breast:
2	chr21:40177627..40180426-chr21:40542526..40544967,2	K562	blood:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1046289	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11700978	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178838	0.84[EUR][1000 genomes]
rs2234545	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297255	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2410103	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836936	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836937	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836941	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836946	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836947	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836962	0.81[EUR][1000 genomes]
rs2836963	0.81[EUR][1000 genomes]
rs2836970	0.84[EUR][1000 genomes]
rs28397992	0.81[EUR][1000 genomes]
rs28552370	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28665841	0.84[EUR][1000 genomes]
rs28693867	0.84[EUR][1000 genomes]
rs28734946	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs376720	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379291	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383965	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420888	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433013	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446090	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816613	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4817994	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4817995	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4817997	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4817998	1.00[EUR][1000 genomes]
rs6517516	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517517	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7278048	0.81[EUR][1000 genomes]
rs7280764	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7281540	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8126528	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8129850	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130798	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305669	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305670	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975909	0.80[EUR][1000 genomes]
rs9977787	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9979936	0.84[EUR][1000 genomes]
rs9981595	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9984518	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9985148	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs449428	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs449428	BRWD1	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40533600-40545400	Weak transcription	HUVEC	blood vessel
2	chr21:40537200-40542800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr21:40537200-40543000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr21:40537200-40543000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr21:40537200-40543000	Weak transcription	Lung	lung
6	chr21:40537200-40543000	Weak transcription	Pancreas	Pancrea
7	chr21:40537400-40543000	Weak transcription	Aorta	Aorta
8	chr21:40537400-40543000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr21:40537400-40543200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr21:40537600-40553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr21:40537800-40543000	Weak transcription	HepG2	liver
12	chr21:40538000-40543000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr21:40538200-40543200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr21:40538400-40542800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr21:40538400-40543000	Weak transcription	Fetal Intestine Small	intestine
16	chr21:40538400-40544800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr21:40538600-40543000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:40538600-40543000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr21:40538800-40542800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr21:40538800-40542800	Weak transcription	K562	blood
21	chr21:40538800-40543000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr21:40538800-40545200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr21:40538800-40550400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr21:40539000-40543000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr21:40539000-40543000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr21:40539000-40550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr21:40539200-40542800	Weak transcription	Fetal Kidney	kidney
28	chr21:40539200-40543000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr21:40539200-40543400	Weak transcription	Brain Anterior Caudate	brain
30	chr21:40539400-40543000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr21:40539400-40544800	Weak transcription	NHDF-Ad	bronchial
32	chr21:40539400-40545200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr21:40540000-40543000	Weak transcription	Ovary	ovary
36	chr21:40540000-40543200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
38	chr21:40540800-40543000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr21:40540800-40543000	Weak transcription	Brain Hippocampus Middle	brain
40	chr21:40540800-40543000	Weak transcription	Fetal Thymus	thymus
41	chr21:40540800-40543000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr21:40540800-40543000	Weak transcription	Spleen	Spleen
43	chr21:40541000-40543000	Weak transcription	Gastric	stomach
44	chr21:40541000-40543000	Weak transcription	Right Ventricle	heart
45	chr21:40541000-40543000	Weak transcription	Osteobl	bone
46	chr21:40541000-40543200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr21:40541000-40543200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr21:40541000-40543200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr21:40541000-40543200	Weak transcription	NH-A	brain
50	chr21:40541000-40543800	Weak transcription	Colonic Mucosa	Colon

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