Variant report

Variant	rs7279558
Chromosome Location	chr21:40692633-40692634
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40690460..40692960-chr21:40749748..40751781,2	K562	blood:
2	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
3	chr21:40692002..40694012-chr22:43010007..43012538,2	MCF-7	breast:
4	chr21:40691963..40695047-chr21:40751458..40754017,3	MCF-7	breast:
5	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205581	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000270022	Chromatin interaction
ENSG00000100227	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1011413	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10154217	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11088471	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11088472	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11910705	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11910906	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11911822	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12626405	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1882779	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1888487	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1888488	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963676	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2005933	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2037925	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272576	0.81[ASN][1000 genomes]
rs2272577	0.83[ASN][1000 genomes]
rs2272578	0.83[ASN][1000 genomes]
rs2297258	0.83[ASN][1000 genomes]
rs2410123	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2410124	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836969	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836971	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836975	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836981	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836982	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836986	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836987	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836988	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34240248	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34436313	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35182074	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35909862	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3746885	0.83[ASN][1000 genomes]
rs3746886	0.83[ASN][1000 genomes]
rs4624474	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4816620	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4816623	0.87[ASN][1000 genomes]
rs4818005	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818015	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4818017	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61300849	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517535	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6517540	0.84[ASN][1000 genomes]
rs6517541	0.84[ASN][1000 genomes]
rs719230	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7276774	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7278985	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7280326	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7281853	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8127986	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8130854	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9636957	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs997147	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9974757	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9975119	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9975562	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9975614	0.82[ASN][1000 genomes]
rs9978775	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9979483	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9981301	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9981656	0.87[ASN][1000 genomes]
rs9982111	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7279558	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs7279558	PSMG1	cis	Esophagus Mucosa	GTEx
rs7279558	PSMG1	cis	lung	GTEx
rs7279558	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs7279558	PSMG1	cis	Artery Tibial	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40687000-40693400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr21:40687600-40693000	Enhancers	Fetal Heart	heart
3	chr21:40689600-40693800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr21:40690600-40692800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr21:40690600-40692800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr21:40690600-40692800	Enhancers	Left Ventricle	heart
7	chr21:40690800-40694600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr21:40692000-40694000	Enhancers	HMEC	breast
9	chr21:40692000-40694200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr21:40692400-40692800	Enhancers	K562	blood
11	chr21:40692400-40693400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:40692400-40693400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr21:40692400-40693400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr21:40692400-40693400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr21:40692400-40693400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr21:40692400-40693400	Weak transcription	A549	lung
17	chr21:40692400-40693400	Weak transcription	Hela-S3	cervix
18	chr21:40692400-40693400	Weak transcription	HepG2	liver
19	chr21:40692400-40693400	Weak transcription	NHDF-Ad	bronchial
20	chr21:40692400-40693400	Weak transcription	NHEK	skin
21	chr21:40692400-40693400	Weak transcription	NHLF	lung
22	chr21:40692400-40693400	Weak transcription	Osteobl	bone
23	chr21:40692400-40693600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr21:40692400-40693600	Active TSS	Placenta	Placenta
25	chr21:40692400-40694400	Weak transcription	HSMMtube	muscle
26	chr21:40692400-40694600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr21:40692400-40718400	Weak transcription	Right Atrium	heart
28	chr21:40692600-40693600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr21:40692600-40694400	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links