Variant report

Variant	rs6517521
Chromosome Location	chr21:40551588-40551589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
2	chr21:40551398..40553559-chr21:40572324..40574736,2	K562	blood:
3	chr21:40550947..40553094-chr21:40816313..40818311,2	MCF-7	breast:
4	chr21:40177078..40179093-chr21:40551455..40553285,2	K562	blood:
5	chr21:40550424..40553042-chr21:40683249..40686279,3	K562	blood:
6	chr21:40551398..40560769-chr21:40565658..40576445,18	K562	blood:

Variant related genes	Relation type
ENSG00000157578	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1041440	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10427502	0.81[AMR][1000 genomes]
rs1065242	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11910151	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11911112	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11911149	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481860	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482156	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482857	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12483216	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12710453	0.88[EUR][1000 genomes]
rs13047550	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13048178	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13049280	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13052882	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13339986	0.89[EUR][1000 genomes]
rs13625	0.82[AMR][1000 genomes]
rs14194	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541102	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1571709	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984022	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2026265	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2142111	0.85[AFR][1000 genomes]
rs2150415	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2234543	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2245455	0.83[AFR][1000 genomes]
rs2836920	0.80[ASN][1000 genomes]
rs2836921	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836923	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836924	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836925	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836927	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836928	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836929	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836932	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836933	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2836938	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2836944	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836953	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2836955	0.84[EUR][1000 genomes]
rs2836957	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836964	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836965	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2836967	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2836968	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836972	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2836973	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2836977	0.82[AMR][1000 genomes]
rs34035316	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34176878	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34294410	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34394827	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433511	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34478864	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34592564	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34978594	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35064900	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35068861	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35386515	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35391055	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571600	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35774464	0.89[EUR][1000 genomes]
rs36113648	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3945	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs428602	0.81[AFR][1000 genomes]
rs4817996	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55836299	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56049536	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56112725	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56306759	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6517513	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517514	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517519	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517523	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6517526	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6517527	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6517533	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6517538	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66465538	0.83[EUR][1000 genomes]
rs68004583	0.81[AMR][1000 genomes]
rs68090597	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71184665	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280375	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282624	0.82[AMR][1000 genomes]
rs7283569	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73221174	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73221193	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354783	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8127087	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128026	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128102	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8128191	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128620	0.82[AMR][1000 genomes]
rs8128734	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8129355	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8129416	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8130556	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8130984	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8131965	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8132295	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132333	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132419	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132568	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133146	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9941894	0.82[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
rs6517521	PSMG1	cis	Muscle Skeletal	GTEx
rs6517521	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs6517521	PSMG1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40537600-40553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
5	chr21:40541200-40552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr21:40541200-40552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr21:40541200-40553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr21:40541200-40553000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
12	chr21:40541400-40553000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr21:40541600-40553800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr21:40541600-40554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:40541600-40554000	Weak transcription	Colon Smooth Muscle	Colon
17	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
18	chr21:40542000-40554000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr21:40542000-40554000	Weak transcription	Stomach Mucosa	stomach
20	chr21:40542200-40551600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
22	chr21:40542800-40554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr21:40543000-40552400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr21:40543000-40552400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr21:40543000-40552600	Strong transcription	Osteobl	bone
26	chr21:40543200-40551800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr21:40543400-40554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr21:40543600-40553200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr21:40543800-40553200	Weak transcription	Small Intestine	intestine
30	chr21:40543800-40554000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr21:40543800-40554000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr21:40543800-40554200	Weak transcription	Right Ventricle	heart
33	chr21:40543800-40554600	Weak transcription	Left Ventricle	heart
34	chr21:40544000-40553800	Weak transcription	HSMMtube	muscle
35	chr21:40544000-40554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr21:40544000-40554000	Weak transcription	Brain Anterior Caudate	brain
37	chr21:40544200-40554000	Weak transcription	Brain Hippocampus Middle	brain
38	chr21:40544200-40554000	Weak transcription	Colonic Mucosa	Colon
39	chr21:40544600-40552400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr21:40544800-40551600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr21:40545400-40552400	Strong transcription	Hela-S3	cervix
42	chr21:40545600-40553000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr21:40545600-40554200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr21:40545800-40553800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr21:40546400-40552400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr21:40546400-40553800	Weak transcription	NHLF	lung
47	chr21:40546400-40554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr21:40546400-40554000	Weak transcription	Brain Angular Gyrus	brain
49	chr21:40546400-40554000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr21:40546400-40554000	Weak transcription	Esophagus	oesophagus

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