Variant report

Variant	rs379291
Chromosome Location	chr21:40547083-40547084
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:40547040-40547511	IMR90	lung:	n/a	n/a
2	CTCF	chr21:40546911-40548103	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr21:40547060-40547210	GM12872	blood:	n/a	n/a
4	RAD21	chr21:40547051-40547618	HCT-116	colon:	n/a	n/a
5	CTCF	chr21:40546960-40547110	GM12864	blood:	n/a	n/a
6	RAD21	chr21:40546976-40547408	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr21:40547014-40547556	HCT-116	colon:	n/a	n/a
8	CTCF	chr21:40546940-40547090	WI-38	lung:	n/a	n/a
9	CTCF	chr21:40547020-40547170	HCT-116	colon:	n/a	n/a
10	CTCF	chr21:40547040-40547190	RPTEC	kidney:	n/a	n/a
11	RAD21	chr21:40546595-40547838	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr21:40547018-40547698	A549	lung:	n/a	n/a
13	POLR2A	chr21:40546956-40547156	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40105428..40106530-chr21:40546782..40547826,4	MCF-7	breast:
2	chr21:40542935..40544954-chr21:40544958..40548517,4	MCF-7	breast:
3	chr21:39731389..39731939-chr21:40546750..40547723,2	MCF-7	breast:
4	chr21:39877751..39878284-chr21:40546921..40547774,2	K562	blood:
5	chr21:40529860..40532688-chr21:40545443..40547905,2	K562	blood:
6	chr21:40544824..40547305-chr21:40554591..40556677,3	MCF-7	breast:

No data

Variant related genes	Relation type
PCBP2P1	TF binding region
ENSG00000183527	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000235701	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1046289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11700978	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554933	0.89[JPT][hapmap]
rs1888490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2178838	0.86[EUR][1000 genomes]
rs2234545	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2410103	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2776311	0.82[CHB][hapmap]
rs2836936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2836970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2836976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2836978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28397992	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2854727	0.81[CHB][hapmap]
rs28552370	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28665841	0.86[EUR][1000 genomes]
rs28693867	0.86[EUR][1000 genomes]
rs28734946	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3761372	0.89[JPT][hapmap]
rs376720	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383965	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433013	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449428	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816613	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4817994	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4817995	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4817997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4817998	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6517516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517522	0.82[CHB][hapmap]
rs7278048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7280764	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7281540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs741795	0.82[CHB][hapmap]
rs8126528	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8129850	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]
rs8130798	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9975909	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9977787	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9977926	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9979691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9979936	0.86[EUR][1000 genomes]
rs9981595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9984518	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9985148	0.86[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
rs379291	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs379291	BRWD1	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40537600-40553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:40538800-40550400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr21:40539000-40550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
7	chr21:40541000-40547600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr21:40541200-40547800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:40541200-40548400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr21:40541200-40550600	Strong transcription	Dnd41	blood
11	chr21:40541200-40552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr21:40541200-40552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr21:40541200-40553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr21:40541200-40553000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
18	chr21:40541400-40553000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr21:40541600-40553800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr21:40541600-40554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:40541600-40554000	Weak transcription	Colon Smooth Muscle	Colon
23	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
24	chr21:40542000-40554000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr21:40542000-40554000	Weak transcription	Stomach Mucosa	stomach
26	chr21:40542200-40551600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr21:40542400-40548600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
29	chr21:40542800-40547400	Weak transcription	Fetal Heart	heart
30	chr21:40542800-40554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr21:40543000-40547600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr21:40543000-40547800	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr21:40543000-40548000	Strong transcription	Fetal Intestine Small	intestine
34	chr21:40543000-40549400	Strong transcription	HepG2	liver
35	chr21:40543000-40552400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr21:40543000-40552400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr21:40543000-40552600	Strong transcription	Osteobl	bone
38	chr21:40543200-40548200	Strong transcription	NH-A	brain
39	chr21:40543200-40549000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr21:40543200-40549400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr21:40543200-40551800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr21:40543400-40554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr21:40543600-40553200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr21:40543800-40550600	Weak transcription	Fetal Kidney	kidney
45	chr21:40543800-40553200	Weak transcription	Small Intestine	intestine
46	chr21:40543800-40554000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr21:40543800-40554000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr21:40543800-40554200	Weak transcription	Right Ventricle	heart
49	chr21:40543800-40554600	Weak transcription	Left Ventricle	heart
50	chr21:40544000-40547600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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