Variant report

Variant	rs1882779
Chromosome Location	chr21:40690938-40690939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr21:40690858-40691130	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr21:40688736-40691506	Raji	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40689203..40691198-chr21:40730612..40733224,2	MCF-7	breast:
2	chr21:40690460..40692960-chr21:40749748..40751781,2	K562	blood:
3	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
4	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
5	chr21:40687654..40692063-chr21:40815994..40821163,6	MCF-7	breast:
6	chr21:40689989..40692160-chr21:41044598..41047094,2	MCF-7	breast:
7	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
8	chr21:40689727..40692043-chr21:41693980..41696191,2	MCF-7	breast:

No data

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

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1011413	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10154217	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11088471	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11088472	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11910705	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11910906	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11911822	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12626405	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1888487	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1888488	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1963676	0.82[AMR][1000 genomes]
rs1984748	0.82[ASN][1000 genomes]
rs2005933	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2037925	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2142117	0.82[ASN][1000 genomes]
rs2410123	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2410124	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836969	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836971	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836975	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836981	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836982	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836986	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836987	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836988	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34240248	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34436313	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35182074	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35909862	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4624474	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4816620	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4818005	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4818014	0.82[ASN][1000 genomes]
rs4818015	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818017	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61300849	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6517535	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517539	0.81[ASN][1000 genomes]
rs719230	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7276559	0.81[ASN][1000 genomes]
rs7276698	0.81[ASN][1000 genomes]
rs7276774	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7278985	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7279558	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7280326	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7281853	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7282724	0.81[ASN][1000 genomes]
rs7283652	0.81[ASN][1000 genomes]
rs8127986	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8130099	0.83[ASN][1000 genomes]
rs8130774	0.81[ASN][1000 genomes]
rs8130854	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8131150	0.83[ASN][1000 genomes]
rs8131307	0.82[ASN][1000 genomes]
rs9636957	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs997147	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9974757	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9975119	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9975562	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9977762	0.81[ASN][1000 genomes]
rs9978775	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9979483	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9981301	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9982111	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1882779	PSMG1	cis	Esophagus Mucosa	GTEx
rs1882779	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs1882779	PSMG1	cis	lung	GTEx
rs1882779	PSMG1	cis	Artery Tibial	GTEx

Chromatin state (count:51 , 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	chr21:40686800-40691200	Weak transcription	Right Ventricle	heart
3	chr21:40686800-40691800	Weak transcription	Right Atrium	heart
4	chr21:40686800-40692200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:40687000-40691000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr21:40687000-40691000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr21:40687000-40691000	Weak transcription	Adipose Nuclei	Adipose
8	chr21:40687000-40691000	Weak transcription	Colon Smooth Muscle	Colon
9	chr21:40687000-40691000	Weak transcription	Hela-S3	cervix
10	chr21:40687000-40691000	Weak transcription	NHLF	lung
11	chr21:40687000-40691200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr21:40687000-40691200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr21:40687000-40691200	Weak transcription	Pancreas	Pancrea
14	chr21:40687000-40691200	Weak transcription	NHDF-Ad	bronchial
15	chr21:40687000-40691200	Weak transcription	Osteobl	bone
16	chr21:40687000-40691800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:40687000-40691800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr21:40687000-40692000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr21:40687000-40693400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr21:40687200-40691200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr21:40687200-40691800	Weak transcription	Fetal Stomach	stomach
22	chr21:40687600-40693000	Enhancers	Fetal Heart	heart
23	chr21:40688200-40691600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr21:40688800-40691200	Weak transcription	HSMM	muscle
25	chr21:40689200-40692000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr21:40689400-40691200	Weak transcription	A549	lung
27	chr21:40689600-40691200	Enhancers	Fetal Lung	lung
28	chr21:40689600-40692000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr21:40689600-40693800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr21:40689800-40691000	Weak transcription	Liver	Liver
31	chr21:40689800-40691200	Weak transcription	NHEK	skin
32	chr21:40689800-40691800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:40689800-40692000	Weak transcription	HMEC	breast
34	chr21:40690000-40691200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr21:40690000-40691200	Enhancers	Placenta	Placenta
36	chr21:40690000-40691200	Weak transcription	Stomach Mucosa	stomach
37	chr21:40690200-40691000	Enhancers	Stomach Smooth Muscle	stomach
38	chr21:40690200-40691600	Enhancers	K562	blood
39	chr21:40690600-40691000	Weak transcription	HepG2	liver
40	chr21:40690600-40691000	Weak transcription	HSMMtube	muscle
41	chr21:40690600-40691200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr21:40690600-40692400	Enhancers	Psoas Muscle	Psoas
43	chr21:40690600-40692800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr21:40690600-40692800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr21:40690600-40692800	Enhancers	Left Ventricle	heart
46	chr21:40690800-40691000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr21:40690800-40692200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr21:40690800-40692400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr21:40690800-40692400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr21:40690800-40692600	Enhancers	Fetal Muscle Leg	muscle

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