Variant report

Variant	rs9982870
Chromosome Location	chr21:40713065-40713066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr21:40712739-40714047	K562	blood:	n/a	n/a
2	POLR2A	chr21:40712648-40714047	HepG2	liver:	n/a	n/a
3	POLR2A	chr21:40712320-40713908	GM12878	blood:	n/a	n/a
4	POLR2A	chr21:40712533-40714043	GM12892	blood:	n/a	n/a
5	POLR2A	chr21:40712664-40714026	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:40712540-40713998	GM12891	blood:	n/a	n/a
7	POLR2A	chr21:40712283-40714096	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr21:40712609-40714043	K562	blood:	n/a	n/a
9	POLR2A	chr21:40712665-40714086	GM19193	blood:	n/a	n/a
10	POLR2A	chr21:40712936-40713979	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr21:40712648-40714029	GM12891	blood:	n/a	n/a
12	POLR2A	chr21:40712617-40713847	HepG2	liver:	n/a	n/a
13	POLR2A	chr21:40713055-40713824	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr21:40712691-40714288	K562	blood:	n/a	n/a
15	POLR2A	chr21:40712641-40713984	K562	blood:	n/a	n/a
16	POLR2A	chr21:40712655-40713946	HepG2	liver:	n/a	n/a
17	POLR2A	chr21:40712599-40714102	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr21:40712660-40713861	HEK293	kidney:	n/a	n/a
19	POLR2A	chr21:40712480-40713812	GM12892	blood:	n/a	n/a
20	POLR2A	chr21:40712618-40713861	PBDE	blood:	n/a	n/a
21	POLR2A	chr21:40712684-40713993	GM12891	blood:	n/a	n/a
22	POLR2A	chr21:40712598-40713249	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr21:40711172-40713994	MCF-7	breast:	n/a	n/a
24	NFATC1	chr21:40712600-40713099	GM12878	blood:	n/a	n/a
25	POLR2A	chr21:40713065-40713959	GM12891	blood:	n/a	n/a
26	POLR2A	chr21:40712500-40713580	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr21:40712881-40714032	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr21:40712445-40714030	HL-60	blood:	n/a	n/a
29	POLR2A	chr21:40712563-40714113	GM12892	blood:	n/a	n/a
30	POLR2A	chr21:40712641-40713800	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr21:40711343-40714219	K562	blood:	n/a	n/a
32	POLR2A	chr21:40712946-40714030	U87	brain:	n/a	n/a
33	POLR2A	chr21:40712234-40713900	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr21:40712249-40714148	GM12878	blood:	n/a	n/a
35	POLR2A	chr21:40712654-40714049	GM12892	blood:	n/a	n/a
36	POLR2A	chr21:40712687-40713334	HL-60	blood:	n/a	n/a
37	POLR2A	chr21:40712533-40713460	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr21:40712494-40714132	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr21:40712706-40714014	GM12892	blood:	n/a	n/a
40	POLR2A	chr21:40712577-40713186	HCT-116	colon:	n/a	n/a
41	POLR2A	chr21:40712468-40713820	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr21:40712280-40714133	GM12891	blood:	n/a	n/a
43	POLR2A	chr21:40712636-40714130	K562	blood:	n/a	n/a
44	POLR2A	chr21:40712637-40713991	K562	blood:	n/a	n/a
45	POLR2A	chr21:40712763-40714119	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr21:40712458-40713892	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr21:40712987-40714172	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr21:40712998-40713920	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr21:40712540-40714059	GM12878	blood:	n/a	n/a
50	POLR2A	chr21:40712571-40713909	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	21:40712819-40717370..21:40748850-40752541	GM12878	blood:
2	chr21:40691885..40693506-chr21:40712326..40714444,2	K562	blood:
3	chr21:40681057..40687929-chr21:40707012..40715318,11	K562	blood:
4	chr21:40646616..40649505-chr21:40712893..40714626,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000252915	TF binding region
ENSG00000238141	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000227406	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10154073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12329720	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12329767	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2070866	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836976	0.83[EUR][1000 genomes]
rs2836978	0.84[EUR][1000 genomes]
rs2836979	0.84[EUR][1000 genomes]
rs28460573	0.84[EUR][1000 genomes]
rs28494168	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28542479	0.84[EUR][1000 genomes]
rs28580194	0.84[EUR][1000 genomes]
rs28590100	0.84[EUR][1000 genomes]
rs28684434	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4818020	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4818026	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130083	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9305673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997146	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9974266	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975256	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9975728	0.84[EUR][1000 genomes]
rs9975937	0.84[EUR][1000 genomes]
rs9976346	0.82[EUR][1000 genomes]
rs9979571	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9979691	0.84[EUR][1000 genomes]
rs9981349	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9981527	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9982825	0.84[EUR][1000 genomes]
rs9984922	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9985067	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9982870	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs9982870	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	chr21:40692400-40718400	Weak transcription	Right Atrium	heart
2	chr21:40704000-40719600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:40704200-40713200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr21:40704400-40713200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40704400-40713400	Weak transcription	Hela-S3	cervix
6	chr21:40704400-40715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr21:40704400-40715200	Weak transcription	Spleen	Spleen
8	chr21:40704600-40713200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr21:40704600-40713200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr21:40704600-40713800	Weak transcription	Ovary	ovary
11	chr21:40704600-40717200	Weak transcription	Right Ventricle	heart
12	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:40704800-40715200	Weak transcription	Fetal Heart	heart
14	chr21:40708800-40713200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr21:40708800-40713400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr21:40708800-40715200	Weak transcription	Gastric	stomach
17	chr21:40709000-40713400	Weak transcription	Stomach Mucosa	stomach
18	chr21:40709600-40713200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr21:40710000-40715200	Weak transcription	Small Intestine	intestine
20	chr21:40710400-40713600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr21:40710400-40715400	Weak transcription	Psoas Muscle	Psoas
22	chr21:40710800-40713200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr21:40711000-40713200	Weak transcription	HUVEC	blood vessel
24	chr21:40711200-40713400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr21:40711400-40713200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr21:40711400-40713200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr21:40711400-40713600	Weak transcription	Brain Hippocampus Middle	brain
28	chr21:40711400-40714200	Weak transcription	Brain Angular Gyrus	brain
29	chr21:40711600-40713400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr21:40711600-40713400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr21:40711600-40713400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr21:40711600-40713600	Weak transcription	NHDF-Ad	bronchial
33	chr21:40711600-40715400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr21:40711800-40713200	Weak transcription	HepG2	liver
35	chr21:40711800-40713400	Weak transcription	Brain Anterior Caudate	brain
36	chr21:40711800-40715000	Weak transcription	NHLF	lung
37	chr21:40711800-40715200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr21:40711800-40715200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr21:40711800-40715200	Weak transcription	Brain Substantia Nigra	brain
40	chr21:40711800-40719600	Weak transcription	Pancreas	Pancrea
41	chr21:40712000-40715200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr21:40712000-40715200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr21:40712000-40715200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr21:40712000-40715200	Weak transcription	Aorta	Aorta
45	chr21:40712000-40717200	Strong transcription	Fetal Stomach	stomach
46	chr21:40712200-40716000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr21:40712200-40716200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr21:40712200-40718800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr21:40712400-40713200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr21:40712400-40715800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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