Variant report

Variant	rs4817999
Chromosome Location	chr21:40554355-40554356
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr21:40554102-40554357	HepG2	liver:	n/a	n/a
2	MAX	chr21:40554104-40556218	NB4	blood:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
3	TBP	chr21:40554331-40556457	K562	blood:	n/a	n/a
4	MAX	chr21:40554338-40556187	Hela-S3	cervix:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
5	MYC	chr21:40554007-40556427	K562	blood:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
6	POLR2A	chr21:40554254-40556348	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr21:40553981-40556152	IMR90	lung:	n/a	n/a
8	TEAD4	chr21:40553883-40556682	K562	blood:	n/a	n/a
9	MXI1	chr21:40553519-40556556	IMR90	lung:	n/a	chr21:40554025-40554034
10	HEY1	chr21:40553995-40556159	K562	blood:	n/a	chr21:40555851-40555866 chr21:40555410-40555425 chr21:40554795-40554810
11	POLR2A	chr21:40554048-40556465	MCF10A-Er-Src	breast:	n/a	n/a
12	MAX	chr21:40554352-40556176	HepG2	liver:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
13	POLR2A	chr21:40554056-40554459	GM12878	blood:	n/a	n/a
14	POLR2A	chr21:40554160-40554665	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F6	chr21:40554096-40556091	K562	blood:	n/a	chr21:40556039-40556053 chr21:40556007-40556016 chr21:40554560-40554572
16	ZMIZ1	chr21:40554195-40554497	K562	blood:	n/a	n/a
17	POLR2A	chr21:40554073-40556379	K562	blood:	n/a	n/a
18	MYC	chr21:40554057-40556055	K562	blood:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
19	EP300	chr21:40554343-40556045	K562	blood:	n/a	n/a
20	MXI1	chr21:40553968-40556305	K562	blood:	n/a	chr21:40554025-40554034
21	POLR2A	chr21:40553945-40556144	HepG2	liver:	n/a	n/a
22	MYC	chr21:40553908-40556596	K562	blood:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
23	POLR2A	chr21:40553940-40554370	GM12878	blood:	n/a	n/a
24	ZNF263	chr21:40554148-40556513	HEK293-T-REx	kidney:	n/a	chr21:40555237-40555258
25	MAZ	chr21:40554093-40556262	IMR90	lung:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
26	SIN3AK20	chr21:40554340-40556881	MCF-7	breast:	n/a	n/a
27	POLR2A	chr21:40554031-40556292	HepG2	liver:	n/a	n/a
28	POLR2A	chr21:40554241-40556221	Hela-S3	cervix:	n/a	n/a
29	MYC	chr21:40554176-40554573	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr21:40553970-40556614	K562	blood:	n/a	n/a
31	MXI1	chr21:40553988-40557071	SK-N-SH	brain:	n/a	chr21:40554025-40554034
32	POLR2A	chr21:40554222-40556451	Raji	blood:	n/a	n/a
33	IRF1	chr21:40553796-40554356	K562	blood:	n/a	n/a
34	BHLHE40	chr21:40554197-40556204	K562	blood:	n/a	chr21:40555869-40555885
35	JUND	chr21:40554322-40554826	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
2	chr21:40554206..40555769-chr21:40571633..40573834,2	K562	blood:
3	chr21:40552516..40555515-chr21:40758943..40760790,2	MCF-7	breast:
4	chr21:40552682..40557546-chr21:40815502..40820280,12	K562	blood:
5	chr21:40553821..40557385-chr21:40719764..40724370,6	K562	blood:
6	chr21:40554325..40556073-chr21:40808791..40811765,2	K562	blood:
7	chr21:40552682..40557091-chr21:40814575..40819975,14	K562	blood:
8	chr21:40175328..40178574-chr21:40554098..40556223,3	K562	blood:
9	chr21:40554013..40557423-chr21:40684520..40688084,3	MCF-7	breast:
10	chr21:40553901..40555576-chr21:40760955..40763916,2	K562	blood:
11	chr21:40552621..40555799-chr21:40758034..40760615,3	K562	blood:
12	chr21:40175328..40180167-chr21:40553641..40558387,7	K562	blood:
13	chr21:40552640..40555791-chr21:40749339..40752310,3	K562	blood:
14	chr21:40553976..40556398-chr21:40816228..40819085,2	MCF-7	breast:
15	chr21:40553454..40557456-chr21:40682892..40687176,12	K562	blood:
16	chr21:40032723..40034705-chr21:40552796..40555245,2	MCF-7	breast:
17	chr21:40551398..40560769-chr21:40565658..40576445,18	K562	blood:

Variant related genes	Relation type
PSMG1	TF binding region
ENSG00000272991	TF binding region
ENSG00000238141	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000157554	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000157578	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1011413	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11910151	0.81[AFR][1000 genomes]
rs11911822	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12626405	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13050247	0.81[ASN][1000 genomes]
rs13052882	0.85[AFR][1000 genomes]
rs1571709	0.86[AFR][1000 genomes]
rs1888487	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1888488	0.82[AMR][1000 genomes]
rs2037925	0.80[AMR][1000 genomes]
rs2142111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2150411	0.85[AFR][1000 genomes]
rs2183573	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2245455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2410123	0.80[AMR][1000 genomes]
rs2836930	0.83[AFR][1000 genomes]
rs2836931	0.83[AFR][1000 genomes]
rs2836969	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836971	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836975	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836981	0.80[AMR][1000 genomes]
rs2836982	0.80[AMR][1000 genomes]
rs2836987	0.80[AMR][1000 genomes]
rs2836988	0.80[AMR][1000 genomes]
rs35909862	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36113648	0.85[AFR][1000 genomes]
rs371625	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs377098	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs383967	0.81[ASN][1000 genomes]
rs391062	0.81[ASN][1000 genomes]
rs413078	0.81[ASN][1000 genomes]
rs414850	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs418298	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs418359	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs419469	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs425988	0.81[ASN][1000 genomes]
rs428602	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs429955	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs442972	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs444130	0.81[ASN][1000 genomes]
rs452377	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452776	0.81[ASN][1000 genomes]
rs4816620	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4818001	0.84[AFR][1000 genomes]
rs4818005	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4818015	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4818017	0.80[AMR][1000 genomes]
rs61300849	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6517520	0.81[ASN][1000 genomes]
rs6517535	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6650847	0.81[ASN][1000 genomes]
rs66519408	0.81[ASN][1000 genomes]
rs66746936	0.81[ASN][1000 genomes]
rs67212994	0.81[ASN][1000 genomes]
rs67649754	0.81[ASN][1000 genomes]
rs68114370	0.81[ASN][1000 genomes]
rs719230	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7276774	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7278985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7281853	0.80[AMR][1000 genomes]
rs7282604	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8127986	0.80[AMR][1000 genomes]
rs8130795	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8130854	0.80[AMR][1000 genomes]
rs9636957	0.80[AMR][1000 genomes]
rs997147	0.80[AMR][1000 genomes]
rs9974757	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9978775	0.80[AMR][1000 genomes]
rs9982111	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9982122	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	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
3	esv3422692	chr21:40554107-40556955	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4817999	PSMG1	cis	lung	GTEx
rs4817999	PSMG1	cis	Nerve Tibial	GTEx
rs4817999	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs4817999	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs4817999	PSMG1	cis	Esophagus Mucosa	GTEx
rs4817999	PSMG1	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
2	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
3	chr21:40543800-40554600	Weak transcription	Left Ventricle	heart
4	chr21:40546400-40554600	Weak transcription	Gastric	stomach
5	chr21:40548400-40554400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr21:40548400-40554600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:40553000-40554400	Flanking Active TSS	Hela-S3	cervix
8	chr21:40553000-40556600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr21:40553400-40554600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:40553400-40554600	Flanking Active TSS	K562	blood
11	chr21:40553600-40554400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr21:40553600-40554400	Flanking Active TSS	HepG2	liver
13	chr21:40553600-40554400	Flanking Active TSS	HUVEC	blood vessel
14	chr21:40553600-40554400	Flanking Active TSS	NHDF-Ad	bronchial
15	chr21:40553600-40554400	Flanking Active TSS	NHEK	skin
16	chr21:40553600-40554600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr21:40553600-40554600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr21:40553600-40554600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr21:40553600-40554800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr21:40553600-40554800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr21:40553600-40554800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr21:40553600-40555000	Flanking Active TSS	Dnd41	blood
23	chr21:40553600-40557200	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr21:40553800-40554400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr21:40553800-40554400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr21:40553800-40554400	Flanking Active TSS	NHLF	lung
27	chr21:40553800-40554600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr21:40553800-40554600	Flanking Active TSS	NH-A	brain
29	chr21:40553800-40555000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr21:40553800-40555200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr21:40553800-40556200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr21:40553800-40557000	Active TSS	GM12878-XiMat	blood
33	chr21:40554000-40554400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr21:40554000-40554400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr21:40554000-40554400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr21:40554000-40554400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr21:40554000-40554400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr21:40554000-40554400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr21:40554000-40554400	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr21:40554000-40554400	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr21:40554000-40554400	Enhancers	Brain Substantia Nigra	brain
42	chr21:40554000-40554400	Flanking Active TSS	Fetal Intestine Large	intestine
43	chr21:40554000-40554400	Enhancers	Placenta	Placenta
44	chr21:40554000-40554400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr21:40554000-40554400	Flanking Active TSS	HMEC	breast
46	chr21:40554000-40554600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr21:40554000-40554600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr21:40554000-40554600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr21:40554000-40554600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr21:40554000-40554600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell

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