Variant report

Variant	rs2836927
Chromosome Location	chr21:40543216-40543217
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: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1041440	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10427502	0.84[AMR][1000 genomes]
rs1065242	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11910151	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11911112	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11911149	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481860	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482156	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482181	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482857	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12483216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12710453	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13047550	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13048178	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13049280	0.89[EUR][1000 genomes]
rs13052882	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13339986	0.88[EUR][1000 genomes]
rs13625	0.86[AMR][1000 genomes]
rs14194	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541102	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1571709	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984022	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026265	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2150415	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2234543	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836920	0.80[ASN][1000 genomes]
rs2836921	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836923	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836924	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836925	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836928	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836929	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836932	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836933	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2836938	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836944	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2836953	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836955	0.82[EUR][1000 genomes]
rs2836957	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2836964	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2836965	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836967	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836968	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2836972	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836973	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836974	0.82[AMR][1000 genomes]
rs2836977	0.86[AMR][1000 genomes]
rs34035316	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34176878	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34294410	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34394827	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433511	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34478864	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34592564	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34672724	0.83[AMR][1000 genomes]
rs34978594	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35064900	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35068861	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35386515	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35391055	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35560196	0.83[AMR][1000 genomes]
rs35571600	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35774464	0.88[EUR][1000 genomes]
rs36113648	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3945	0.98[EUR][1000 genomes]
rs4817996	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55836299	0.86[AMR][1000 genomes]
rs56049536	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56112725	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56306759	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6517513	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517514	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517521	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517523	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6517526	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6517527	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6517533	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517538	0.84[AMR][1000 genomes]
rs66465538	0.81[EUR][1000 genomes]
rs68004583	0.84[AMR][1000 genomes]
rs68090597	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71184665	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280375	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282624	0.86[AMR][1000 genomes]
rs7283569	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73221174	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73221193	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354783	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8127087	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128026	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128102	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8128191	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128620	0.86[AMR][1000 genomes]
rs8128734	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8128894	0.83[AMR][1000 genomes]
rs8129355	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8129416	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8130556	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8130984	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8131965	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8132295	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132333	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132419	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132568	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133146	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8134733	0.82[AMR][1000 genomes]
rs9941894	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2836927	PSMG1	cis	Muscle Skeletal	GTEx
rs2836927	PSMG1	cis	Esophagus Mucosa	GTEx
rs2836927	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 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	chr21:40539200-40543400	Weak transcription	Brain Anterior Caudate	brain
8	chr21:40539400-40544800	Weak transcription	NHDF-Ad	bronchial
9	chr21:40539400-40545200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
13	chr21:40541000-40543800	Weak transcription	Colonic Mucosa	Colon
14	chr21:40541000-40544000	Strong transcription	HSMM	muscle
15	chr21:40541000-40547000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr21:40541000-40547600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr21:40541200-40543400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr21:40541200-40543600	Strong transcription	Left Ventricle	heart
19	chr21:40541200-40543800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr21:40541200-40543800	Strong transcription	GM12878-XiMat	blood
21	chr21:40541200-40544000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr21:40541200-40544000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr21:40541200-40544000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr21:40541200-40544400	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr21:40541200-40545400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr21:40541200-40545600	Weak transcription	Fetal Lung	lung
27	chr21:40541200-40546400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr21:40541200-40546400	Strong transcription	Adipose Nuclei	Adipose
29	chr21:40541200-40546400	Strong transcription	Fetal Muscle Leg	muscle
30	chr21:40541200-40546600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr21:40541200-40546600	Strong transcription	Thymus	Thymus
32	chr21:40541200-40547800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr21:40541200-40548400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr21:40541200-40550600	Strong transcription	Dnd41	blood
35	chr21:40541200-40552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr21:40541200-40552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr21:40541200-40553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr21:40541200-40553000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
42	chr21:40541400-40544000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr21:40541400-40545400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr21:40541400-40545400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr21:40541400-40545800	Weak transcription	Brain Angular Gyrus	brain
46	chr21:40541400-40546400	Strong transcription	Fetal Stomach	stomach
47	chr21:40541400-40546800	Strong transcription	A549	lung
48	chr21:40541400-40553000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr21:40541600-40543400	Weak transcription	Esophagus	oesophagus
50	chr21:40541600-40545400	Weak transcription	Hela-S3	cervix

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