Variant report

Variant	rs62223039
Chromosome Location	chr21:40664188-40664189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr21:40660582..40664374-chr21:40667695..40671151,4	MCF-7	breast:
2	chr21:40637761..40639726-chr21:40663827..40665594,2	K562	blood:
3	chr21:40658176..40660368-chr21:40662775..40665528,2	MCF-7	breast:
4	chr21:40647474..40653272-chr21:40661501..40665545,6	K562	blood:
5	chr21:40637950..40639726-chr21:40663827..40665338,2	K562	blood:
6	chr21:40648027..40649939-chr21:40662663..40664806,2	K562	blood:
7	chr21:40663279..40665811-chr21:40674696..40676596,2	K562	blood:
8	chr21:40553804..40556264-chr21:40663046..40664609,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction
ENSG00000183527	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1029004	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10854396	0.83[ASN][1000 genomes]
rs11088466	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11088470	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11701805	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11702505	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11910232	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11911087	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12483559	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12627205	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13047518	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13049907	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1474490	0.83[EUR][1000 genomes]
rs1980407	0.83[EUR][1000 genomes]
rs2056844	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2070865	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2150411	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2150413	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2150414	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297256	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836926	0.83[EUR][1000 genomes]
rs2836930	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2836931	0.83[EUR][1000 genomes]
rs2836934	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836940	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836942	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836943	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836945	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836948	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836949	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836952	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836956	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836958	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836959	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836966	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836980	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2836983	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836984	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836985	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3171465	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34705151	0.82[EUR][1000 genomes]
rs34890172	0.83[EUR][1000 genomes]
rs35769610	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35994303	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4816617	0.83[EUR][1000 genomes]
rs4816618	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818001	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4818018	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4818019	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59916147	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62223011	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62223052	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7276046	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7278297	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7279497	0.83[EUR][1000 genomes]
rs7282582	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8127379	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8129595	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8130162	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8130240	0.83[EUR][1000 genomes]
rs8130320	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8131132	0.83[EUR][1000 genomes]
rs8132143	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8132424	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8133928	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8134214	0.83[EUR][1000 genomes]
rs8134843	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs62223039	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs62223039	HMGN1	cis	multi-tissue	Pritchard
rs62223039	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs62223039	PSMG1	cis	Artery Tibial	GTEx
rs62223039	HMGN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:40638200-40665000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:40638600-40665600	Weak transcription	Spleen	Spleen
4	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
5	chr21:40643800-40684200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:40646600-40683400	Weak transcription	Fetal Brain Male	brain
7	chr21:40650200-40671600	Weak transcription	Aorta	Aorta
8	chr21:40651400-40671600	Weak transcription	Pancreas	Pancrea
9	chr21:40655000-40669400	Strong transcription	NHDF-Ad	bronchial
10	chr21:40655000-40676800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr21:40655000-40683000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr21:40655400-40683200	Strong transcription	Dnd41	blood
13	chr21:40655600-40671800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr21:40655800-40671800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr21:40655800-40672200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr21:40655800-40672800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr21:40655800-40673800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr21:40655800-40677400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr21:40655800-40677400	Strong transcription	Fetal Thymus	thymus
20	chr21:40656000-40669400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr21:40656200-40672400	Strong transcription	Liver	Liver
22	chr21:40656200-40672600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr21:40656200-40674200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr21:40656400-40670200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr21:40656400-40675400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr21:40656400-40676600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr21:40656400-40676800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr21:40656400-40683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr21:40656600-40671600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr21:40658800-40666400	Strong transcription	Primary B cells from cord blood	blood
31	chr21:40658800-40669000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr21:40658800-40670600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr21:40658800-40672000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr21:40658800-40672000	Strong transcription	Adipose Nuclei	Adipose
35	chr21:40659000-40673600	Strong transcription	Hela-S3	cervix
36	chr21:40659200-40674600	Strong transcription	K562	blood
37	chr21:40659400-40668000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr21:40659400-40669800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr21:40659600-40667800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr21:40659600-40670800	Strong transcription	HepG2	liver
41	chr21:40659600-40671800	Strong transcription	Fetal Muscle Leg	muscle
42	chr21:40659600-40676800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr21:40659600-40676800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr21:40659800-40667000	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr21:40659800-40667800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr21:40659800-40669000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr21:40659800-40669400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr21:40659800-40672800	Strong transcription	NH-A	brain
49	chr21:40660000-40664400	Weak transcription	Colon Smooth Muscle	Colon
50	chr21:40660000-40666000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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