Variant report

Variant	rs420888
Chromosome Location	chr21:40543577-40543578
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSMG1-10	chr21:40543056-40544032	NONHSAT082151

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1013129	0.84[CHD][hapmap]
rs1046289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11700978	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554933	0.89[JPT][hapmap]
rs1882777	0.84[CHD][hapmap]
rs1888490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2142112	0.82[CHD][hapmap]
rs2178838	0.86[EUR][1000 genomes]
rs2234545	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2410103	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2776311	0.81[CHB][hapmap]
rs2836936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[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];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[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];0.84[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[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2836990	0.89[JPT][hapmap]
rs28397992	0.84[EUR][1000 genomes]
rs2854727	0.81[CHB][hapmap]
rs28552370	1.00[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	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs376720	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379291	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]
rs383965	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433013	1.00[AFR][1000 genomes];0.90[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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449428	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816613	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4817994	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4817995	0.80[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];0.82[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[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[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];0.82[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];0.84[EUR][1000 genomes]
rs7280764	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7281540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs741795	0.81[CHB][hapmap]
rs8126528	0.80[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130798	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132993	0.81[CHB][hapmap]
rs9305665	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs9305669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305670	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9975909	0.83[EUR][1000 genomes]
rs9977787	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9977926	0.81[EUR][1000 genomes]
rs9979691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap]
rs9979936	0.86[EUR][1000 genomes]
rs9981595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9984518	0.90[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs420888	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs420888	BRWD1	cis	cerebellum	SCAN
rs420888	CBR3	cis	cerebellum	SCAN
rs420888	HMGN1	cis	lymphoblastoid	seeQTL
rs420888	BRWD1	cis	parietal	SCAN
rs420888	BRWD1	cis	multi-tissue	Pritchard
rs420888	CBR1	cis	parietal	SCAN

Chromatin state (count:121 , 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	chr21:40537600-40553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr21:40538400-40544800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr21:40538800-40545200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr21:40538800-40550400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr21:40539000-40550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr21:40539400-40544800	Weak transcription	NHDF-Ad	bronchial
8	chr21:40539400-40545200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
12	chr21:40541000-40543800	Weak transcription	Colonic Mucosa	Colon
13	chr21:40541000-40544000	Strong transcription	HSMM	muscle
14	chr21:40541000-40547000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr21:40541000-40547600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr21:40541200-40543600	Strong transcription	Left Ventricle	heart
17	chr21:40541200-40543800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr21:40541200-40543800	Strong transcription	GM12878-XiMat	blood
19	chr21:40541200-40544000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr21:40541200-40544000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr21:40541200-40544000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr21:40541200-40544400	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr21:40541200-40545400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr21:40541200-40545600	Weak transcription	Fetal Lung	lung
25	chr21:40541200-40546400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr21:40541200-40546400	Strong transcription	Adipose Nuclei	Adipose
27	chr21:40541200-40546400	Strong transcription	Fetal Muscle Leg	muscle
28	chr21:40541200-40546600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr21:40541200-40546600	Strong transcription	Thymus	Thymus
30	chr21:40541200-40547800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr21:40541200-40548400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr21:40541200-40550600	Strong transcription	Dnd41	blood
33	chr21:40541200-40552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr21:40541200-40552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr21:40541200-40553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr21:40541200-40553000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
40	chr21:40541400-40544000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr21:40541400-40545400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr21:40541400-40545400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr21:40541400-40545800	Weak transcription	Brain Angular Gyrus	brain
44	chr21:40541400-40546400	Strong transcription	Fetal Stomach	stomach
45	chr21:40541400-40546800	Strong transcription	A549	lung
46	chr21:40541400-40553000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr21:40541600-40545400	Weak transcription	Hela-S3	cervix
48	chr21:40541600-40545800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr21:40541600-40553800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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