Variant report

Variant	rs28542479
Chromosome Location	chr21:40672344-40672345
allele	A/G
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40664381..40666644-chr21:40671132..40672895,2	K562	blood:
2	21:40671591-40673895..21:40757151-40764378	GM12878	blood:
3	21:40565363-40575691..21:40671591-40673895	GM12878	blood:
4	chr21:40666937..40669991-chr21:40672116..40674107,3	MCF-7	breast:
5	chr21:40671119..40673164-chr21:40679954..40681992,2	K562	blood:
6	chr21:40671338..40675047-chr21:40676117..40679838,4	K562	blood:
7	chr21:40641417..40644269-chr21:40672287..40675035,2	MCF-7	breast:
8	21:40583765-40590917..21:40671591-40673895	GM12878	blood:
9	21:40549407-40551424..21:40671591-40673895	GM12878	blood:
10	21:40671591-40673895..21:40748850-40752541	Hela-S3	cervix:
11	chr21:40671488..40672356-chr21:40760178..40761118,2	MCF-7	breast:
12	chr21:40581211..40583569-chr21:40670765..40672444,2	K562	blood:
13	chr21:40670757..40673579-chr21:40719041..40722481,3	K562	blood:
14	chr21:40671195..40673748-chr21:40675125..40678603,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000205581	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000232608	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10154073	0.84[EUR][1000 genomes]
rs12329720	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12329767	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070866	0.83[EUR][1000 genomes]
rs2178838	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234545	0.81[EUR][1000 genomes]
rs2836941	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836946	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836947	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836962	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836963	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836970	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836976	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836979	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397992	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28460573	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28494168	0.87[EUR][1000 genomes]
rs28580194	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];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28665841	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28684434	0.87[EUR][1000 genomes]
rs28693867	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734946	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4818020	0.84[EUR][1000 genomes]
rs4818026	0.84[EUR][1000 genomes]
rs7278048	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130083	0.83[EUR][1000 genomes]
rs9284464	0.84[EUR][1000 genomes]
rs9305673	0.83[EUR][1000 genomes]
rs997146	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9974266	0.83[EUR][1000 genomes]
rs9975256	0.87[EUR][1000 genomes]
rs9975728	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975909	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9975937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9976346	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977787	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9977926	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979571	0.84[EUR][1000 genomes]
rs9979691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979936	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981349	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9981527	0.83[EUR][1000 genomes]
rs9982825	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9982870	0.84[EUR][1000 genomes]
rs9984518	0.86[ASN][1000 genomes]
rs9984922	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9985067	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9985148	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	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
4	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
5	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
rs28542479	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs28542479	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	chr21:40641400-40683800	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	chr21:40655000-40676800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr21:40655000-40683000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:40655400-40683200	Strong transcription	Dnd41	blood
7	chr21:40655800-40672800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr21:40655800-40673800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr21:40655800-40677400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr21:40655800-40677400	Strong transcription	Fetal Thymus	thymus
11	chr21:40656200-40672400	Strong transcription	Liver	Liver
12	chr21:40656200-40672600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr21:40656200-40674200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr21:40656400-40675400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr21:40656400-40676600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr21:40656400-40676800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr21:40656400-40683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr21:40659000-40673600	Strong transcription	Hela-S3	cervix
19	chr21:40659200-40674600	Strong transcription	K562	blood
20	chr21:40659600-40676800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr21:40659600-40676800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr21:40659800-40672800	Strong transcription	NH-A	brain
23	chr21:40661800-40683400	Weak transcription	Stomach Mucosa	stomach
24	chr21:40662400-40675400	Strong transcription	Osteobl	bone
25	chr21:40662600-40673800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr21:40663000-40672600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr21:40663000-40672800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr21:40663600-40683400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr21:40663800-40672600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr21:40663800-40673000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr21:40663800-40676600	Strong transcription	Left Ventricle	heart
32	chr21:40664000-40684200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr21:40664200-40672800	Strong transcription	HSMM	muscle
34	chr21:40664400-40672400	Strong transcription	Colon Smooth Muscle	Colon
35	chr21:40665000-40683800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr21:40665200-40684400	Weak transcription	Colonic Mucosa	Colon
37	chr21:40666000-40682600	Weak transcription	NHLF	lung
38	chr21:40667000-40684000	Weak transcription	HSMMtube	muscle
39	chr21:40667000-40684200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr21:40667200-40673800	Strong transcription	NHEK	skin
41	chr21:40668600-40673600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr21:40669200-40684200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr21:40669400-40676600	Strong transcription	Fetal Intestine Large	intestine
44	chr21:40669400-40684000	Weak transcription	HUVEC	blood vessel
45	chr21:40669400-40684400	Weak transcription	Esophagus	oesophagus
46	chr21:40669800-40673200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr21:40669800-40673400	Weak transcription	Brain Angular Gyrus	brain
48	chr21:40669800-40676400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr21:40669800-40679800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr21:40669800-40683800	Weak transcription	Brain Substantia Nigra	brain

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