Variant report

Variant	rs2836977
Chromosome Location	chr21:40666066-40666067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40664381..40666644-chr21:40671132..40672895,2	K562	blood:
2	chr21:40660622..40662846-chr21:40664648..40666814,2	K562	blood:
3	chr21:40651393..40653585-chr21:40665831..40668070,2	K562	blood:
4	chr21:40665688..40667750-chr21:40683935..40686161,2	K562	blood:
5	chr21:40661282..40662846-chr21:40664648..40666203,2	K562	blood:

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1041440	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10427502	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1065242	0.86[AMR][1000 genomes]
rs11910151	0.82[AMR][1000 genomes]
rs12151994	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12481860	0.86[AMR][1000 genomes]
rs12482181	0.82[AMR][1000 genomes]
rs12483216	0.86[AMR][1000 genomes]
rs12710453	0.89[EUR][1000 genomes]
rs12710454	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13047663	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13047678	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13048178	0.84[AMR][1000 genomes]
rs13049280	0.88[EUR][1000 genomes]
rs13052882	0.83[AMR][1000 genomes]
rs13339986	0.89[EUR][1000 genomes]
rs13625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs14194	0.82[AMR][1000 genomes]
rs1541102	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1571709	0.82[AMR][1000 genomes]
rs1984022	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2026265	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2026267	0.89[AMR][1000 genomes]
rs2150415	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2234543	0.84[AMR][1000 genomes]
rs2735306	0.89[AMR][1000 genomes]
rs2735309	0.89[AMR][1000 genomes]
rs2776307	0.89[AMR][1000 genomes]
rs2776308	0.89[AMR][1000 genomes]
rs2776309	0.89[AMR][1000 genomes]
rs28360661	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836923	0.82[AMR][1000 genomes]
rs2836925	0.86[AMR][1000 genomes]
rs2836927	0.86[AMR][1000 genomes]
rs2836929	0.84[AMR][1000 genomes]
rs2836932	0.83[AMR][1000 genomes]
rs2836933	0.87[AMR][1000 genomes]
rs2836938	0.87[AMR][1000 genomes]
rs2836944	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2836953	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836955	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836957	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836964	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836965	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836967	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836968	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836972	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836973	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836974	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34035316	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34176878	0.81[AMR][1000 genomes]
rs34294410	0.86[AMR][1000 genomes]
rs34394827	0.80[AMR][1000 genomes]
rs34433511	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34578707	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34672724	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34978594	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35068861	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35123057	0.89[AMR][1000 genomes]
rs35386515	0.84[AMR][1000 genomes]
rs35560196	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35571600	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35774464	0.82[EUR][1000 genomes]
rs36113648	0.85[AMR][1000 genomes]
rs55836299	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56049536	0.82[AMR][1000 genomes]
rs56306759	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6517519	0.86[AMR][1000 genomes]
rs6517521	0.82[AMR][1000 genomes]
rs6517523	0.86[AMR][1000 genomes]
rs6517526	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6517527	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6517533	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6517538	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66465538	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68004583	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68090597	0.86[AMR][1000 genomes]
rs71184665	0.80[AMR][1000 genomes]
rs7277978	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7280375	0.83[AMR][1000 genomes]
rs7282624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7283420	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7283516	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7283569	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73221174	0.82[AMR][1000 genomes]
rs73221193	0.83[AMR][1000 genomes]
rs7354783	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8127087	0.84[AMR][1000 genomes]
rs8128026	0.87[AMR][1000 genomes]
rs8128102	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8128620	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8128734	0.84[AMR][1000 genomes]
rs8128827	0.89[AMR][1000 genomes]
rs8128894	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8129147	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8129303	0.89[AMR][1000 genomes]
rs8129355	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8129416	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8130984	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8131965	0.86[AMR][1000 genomes]
rs8133146	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8134733	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9941894	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2836977	PSMG1	cis	Muscle Skeletal	GTEx
rs2836977	PSMG1	cis	Artery Tibial	GTEx
rs2836977	PSMG1	cis	Esophagus Mucosa	GTEx
rs2836977	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2836977	PSMG1	cis	lung	GTEx
rs2836977	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	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
3	chr21:40643800-40684200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:40646600-40683400	Weak transcription	Fetal Brain Male	brain
5	chr21:40650200-40671600	Weak transcription	Aorta	Aorta
6	chr21:40651400-40671600	Weak transcription	Pancreas	Pancrea
7	chr21:40655000-40669400	Strong transcription	NHDF-Ad	bronchial
8	chr21:40655000-40676800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr21:40655000-40683000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr21:40655400-40683200	Strong transcription	Dnd41	blood
11	chr21:40655600-40671800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr21:40655800-40671800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr21:40655800-40672200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr21:40655800-40672800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr21:40655800-40673800	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr21:40655800-40677400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr21:40655800-40677400	Strong transcription	Fetal Thymus	thymus
18	chr21:40656000-40669400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr21:40656200-40672400	Strong transcription	Liver	Liver
20	chr21:40656200-40672600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr21:40656200-40674200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr21:40656400-40670200	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr21:40656400-40675400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr21:40656400-40676600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr21:40656400-40676800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr21:40656400-40683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr21:40656600-40671600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr21:40658800-40666400	Strong transcription	Primary B cells from cord blood	blood
29	chr21:40658800-40669000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr21:40658800-40670600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr21:40658800-40672000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr21:40658800-40672000	Strong transcription	Adipose Nuclei	Adipose
33	chr21:40659000-40673600	Strong transcription	Hela-S3	cervix
34	chr21:40659200-40674600	Strong transcription	K562	blood
35	chr21:40659400-40668000	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr21:40659400-40669800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr21:40659600-40667800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr21:40659600-40670800	Strong transcription	HepG2	liver
39	chr21:40659600-40671800	Strong transcription	Fetal Muscle Leg	muscle
40	chr21:40659600-40676800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr21:40659600-40676800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr21:40659800-40667000	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr21:40659800-40667800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr21:40659800-40669000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr21:40659800-40669400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr21:40659800-40672800	Strong transcription	NH-A	brain
47	chr21:40660000-40669400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr21:40660800-40668400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr21:40661000-40667800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr21:40661000-40668600	Strong transcription	Fetal Lung	lung

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