Variant report

Variant	rs12329720
Chromosome Location	chr21:40689757-40689758
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:11)
LncRNA
region (count:1)
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	SMARCB1	chr21:40689015-40690576	K562	blood:	n/a	n/a
2	POLR2A	chr21:40689533-40689789	K562	blood:	n/a	n/a
3	CCNT2	chr21:40689146-40689764	K562	blood:	n/a	n/a
4	SPI1	chr21:40689312-40689780	HL-60	blood:	n/a	n/a
5	ATF1	chr21:40689233-40689841	K562	blood:	n/a	n/a
6	ZNF384	chr21:40689398-40690094	K562	blood:	n/a	n/a
7	USF1	chr21:40689279-40689915	K562	blood:	n/a	chr21:40689609-40689620
8	USF2	chr21:40689034-40689831	K562	blood:	n/a	n/a
9	CEBPB	chr21:40689338-40689768	K562	blood:	n/a	n/a
10	MAZ	chr21:40689282-40689882	K562	blood:	n/a	n/a
11	SPI1	chr21:40689021-40689791	GM12878	blood:	n/a	n/a
12	CEBPB	chr21:40689125-40689869	MCF-7	breast:	n/a	n/a
13	UBTF	chr21:40689323-40689902	K562	blood:	n/a	n/a
14	SPI1	chr21:40689169-40689850	HL-60	blood:	n/a	n/a
15	POLR2A	chr21:40688821-40689902	K562	blood:	n/a	n/a
16	SIN3AK20	chr21:40688907-40690039	MCF-7	breast:	n/a	n/a
17	MYC	chr21:40689023-40689937	K562	blood:	n/a	n/a
18	EP300	chr21:40689080-40689766	MCF-7	breast:	n/a	n/a
19	GATA3	chr21:40689028-40689910	MCF-7	breast:	n/a	n/a
20	CTCF	chr21:40689303-40689990	K562	blood:	n/a	n/a
21	MAX	chr21:40689089-40690070	MCF-7	breast:	n/a	n/a
22	UBTF	chr21:40689091-40689868	K562	blood:	n/a	n/a
23	TBP	chr21:40689203-40689838	K562	blood:	n/a	n/a
24	CUX1	chr21:40689100-40690060	K562	blood:	n/a	n/a
25	POLR2A	chr21:40688736-40691506	Raji	blood:	n/a	n/a
26	ELF1	chr21:40689316-40689887	K562	blood:	n/a	n/a
27	JUND	chr21:40688880-40689900	K562	blood:	n/a	n/a
28	HCFC1	chr21:40689119-40689842	K562	blood:	n/a	n/a
29	EP300	chr21:40689430-40689791	GM12878	blood:	n/a	n/a
30	MAX	chr21:40689427-40689812	K562	blood:	n/a	n/a
31	IRF1	chr21:40689074-40689881	K562	blood:	n/a	n/a
32	NR2F2	chr21:40689070-40689827	MCF-7	breast:	n/a	n/a
33	POLR2A	chr21:40689307-40689882	K562	blood:	n/a	n/a
34	ARID3A	chr21:40689214-40689807	K562	blood:	n/a	n/a
35	MAFK	chr21:40688994-40689858	K562	blood:	n/a	n/a
36	USF1	chr21:40689385-40689858	K562	blood:	n/a	chr21:40689609-40689620
37	RCOR1	chr21:40689166-40689951	K562	blood:	n/a	n/a
38	ZNF143	chr21:40689264-40690243	K562	blood:	n/a	n/a
39	BHLHE40	chr21:40689081-40689880	K562	blood:	n/a	n/a
40	REST	chr21:40689369-40689803	K562	blood:	n/a	n/a
41	GATA3	chr21:40688915-40689842	MCF-7	breast:	n/a	n/a
42	SPI1	chr21:40689293-40689785	GM12891	blood:	n/a	n/a
43	MAX	chr21:40689195-40689878	K562	blood:	n/a	n/a
44	KAP1	chr21:40688969-40689994	HEK293	kidney:	n/a	n/a
45	TAL1	chr21:40689269-40689826	K562	blood:	n/a	n/a
46	EP300	chr21:40689186-40690223	K562	blood:	n/a	n/a
47	HEY1	chr21:40689364-40689885	K562	blood:	n/a	n/a
48	TEAD4	chr21:40688942-40690558	K562	blood:	n/a	n/a
49	HDAC2	chr21:40689089-40689955	MCF-7	breast:	n/a	n/a
50	HDAC2	chr21:40689114-40689814	MCF-7	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	21:40687235-40690033..21:40757151-40764378	K562	blood:
2	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
3	chr21:40689203..40691198-chr21:40730612..40733224,2	MCF-7	breast:
4	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
5	chr21:40581217..40582784-chr21:40687990..40689879,2	K562	blood:
6	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
7	chr21:40684466..40689800-chr21:40758261..40763098,10	K562	blood:
8	chr21:40687654..40692063-chr21:40815994..40821163,6	MCF-7	breast:
9	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
10	chr21:40689727..40692043-chr21:41693980..41696191,2	MCF-7	breast:
11	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRB-2	chr21:40688971-40689880	XLOC_013942

No data

Variant related genes	Relation type
BRWD1	TF binding region
BRWD1-IT2	TF binding region
ENSG00000252915	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000238556	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10154073	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12329767	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070866	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2178838	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836941	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836946	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836947	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836962	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836963	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836970	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836976	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836978	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836979	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28397992	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28460573	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494168	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28542479	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28580194	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28590100	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665841	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28684434	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28693867	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28734946	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818020	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4818026	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7278048	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8130083	0.85[EUR][1000 genomes]
rs9284464	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9305673	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs997146	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9974266	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9975256	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9975728	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9975909	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9975937	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9976346	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9977787	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9977926	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9979571	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9979691	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979936	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9981349	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981527	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9982825	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9982870	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9984518	0.81[ASN][1000 genomes]
rs9984922	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9985067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9985148	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv587482	chr21:40684427-40706594	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12329720	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs12329720	BRWD1	cis	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40686600-40691400	Enhancers	Primary B cells from peripheral blood	blood
2	chr21:40686800-40689800	Enhancers	NHEK	skin
3	chr21:40686800-40690600	Weak transcription	Psoas Muscle	Psoas
4	chr21:40686800-40691200	Weak transcription	Right Ventricle	heart
5	chr21:40686800-40691800	Weak transcription	Right Atrium	heart
6	chr21:40686800-40692200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:40687000-40689800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:40687000-40689800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr21:40687000-40689800	Enhancers	HMEC	breast
10	chr21:40687000-40690400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr21:40687000-40690600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr21:40687000-40690600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr21:40687000-40690800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr21:40687000-40691000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr21:40687000-40691000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr21:40687000-40691000	Weak transcription	Adipose Nuclei	Adipose
17	chr21:40687000-40691000	Weak transcription	Colon Smooth Muscle	Colon
18	chr21:40687000-40691000	Weak transcription	Hela-S3	cervix
19	chr21:40687000-40691000	Weak transcription	NHLF	lung
20	chr21:40687000-40691200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr21:40687000-40691200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr21:40687000-40691200	Weak transcription	Pancreas	Pancrea
23	chr21:40687000-40691200	Weak transcription	NHDF-Ad	bronchial
24	chr21:40687000-40691200	Weak transcription	Osteobl	bone
25	chr21:40687000-40691800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr21:40687000-40691800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr21:40687000-40692000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr21:40687000-40693400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr21:40687200-40690200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr21:40687200-40690200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr21:40687200-40690800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr21:40687200-40690800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr21:40687200-40690800	Weak transcription	Fetal Muscle Leg	muscle
34	chr21:40687200-40691200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr21:40687200-40691800	Weak transcription	Fetal Stomach	stomach
36	chr21:40687400-40690600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr21:40687600-40693000	Enhancers	Fetal Heart	heart
38	chr21:40688200-40691600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr21:40688600-40689800	Enhancers	Placenta	Placenta
40	chr21:40688600-40690400	Weak transcription	HSMMtube	muscle
41	chr21:40688800-40691200	Weak transcription	HSMM	muscle
42	chr21:40689000-40689800	Enhancers	Liver	Liver
43	chr21:40689000-40690000	Enhancers	Fetal Intestine Large	intestine
44	chr21:40689000-40690000	Enhancers	Fetal Intestine Small	intestine
45	chr21:40689000-40690000	Enhancers	Stomach Mucosa	stomach
46	chr21:40689000-40690600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr21:40689000-40690600	Enhancers	HepG2	liver
48	chr21:40689200-40689800	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr21:40689200-40690000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr21:40689200-40690200	Flanking Active TSS	K562	blood

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