Variant report

Variant	rs6517533
Chromosome Location	chr21:40643190-40643191
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40631221..40636644-chr21:40641722..40645540,5	MCF-7	breast:
2	chr21:40641417..40644269-chr21:40672287..40675035,2	MCF-7	breast:

Extended variants
information (count: 121 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1041440	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427502	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1065242	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11910151	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11911112	0.80[AMR][1000 genomes]
rs11911149	0.80[AMR][1000 genomes]
rs12151994	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12481860	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12482181	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12483216	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12710453	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710454	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13047663	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13047678	0.81[EUR][1000 genomes]
rs13048178	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13049280	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13052882	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13339986	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13625	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs14194	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1541102	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571709	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1984022	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2026265	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2026267	0.87[AMR][1000 genomes]
rs2150415	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2234543	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2735306	0.87[AMR][1000 genomes]
rs2735309	0.87[AMR][1000 genomes]
rs2776307	0.87[AMR][1000 genomes]
rs2776308	0.87[AMR][1000 genomes]
rs2776309	0.87[AMR][1000 genomes]
rs28360661	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836923	0.83[AMR][1000 genomes]
rs2836924	0.80[AMR][1000 genomes]
rs2836925	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836927	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836928	0.81[EUR][1000 genomes]
rs2836929	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2836932	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2836933	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836938	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2836944	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836953	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2836955	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836957	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836964	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836965	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836967	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836972	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836973	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836974	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836977	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34035316	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34176878	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34294410	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34394827	0.82[AMR][1000 genomes]
rs34433511	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34478864	0.80[AMR][1000 genomes]
rs34578707	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672724	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34978594	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35064900	0.81[EUR][1000 genomes]
rs35068861	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123057	0.87[AMR][1000 genomes]
rs35386515	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35391055	0.80[AMR][1000 genomes]
rs35560196	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571600	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36113648	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3945	0.84[EUR][1000 genomes]
rs4817996	0.80[AMR][1000 genomes]
rs55836299	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56049536	0.83[AMR][1000 genomes]
rs56306759	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6517513	0.80[AMR][1000 genomes]
rs6517519	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517521	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6517523	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517526	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517527	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517538	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66465538	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004583	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68090597	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71184665	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7277978	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7280375	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7282624	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283420	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283516	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283569	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73221174	0.83[AMR][1000 genomes]
rs73221193	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7354783	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127087	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8128026	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8128102	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128191	0.80[AMR][1000 genomes]
rs8128620	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128734	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8128827	0.87[AMR][1000 genomes]
rs8128894	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129147	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8129303	0.87[AMR][1000 genomes]
rs8129355	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129416	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8130984	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8131965	0.87[AMR][1000 genomes]
rs8132295	0.80[AMR][1000 genomes]
rs8132333	0.80[AMR][1000 genomes]
rs8132419	0.80[AMR][1000 genomes]
rs8132568	0.80[AMR][1000 genomes]
rs8133146	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8134733	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941894	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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
rs6517533	PSMG1	cis	lung	GTEx
rs6517533	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs6517533	PSMG1	cis	Esophagus Mucosa	GTEx
rs6517533	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs6517533	PSMG1	cis	Muscle Skeletal	GTEx
rs6517533	PSMG1	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr21:40565400-40653600	Strong transcription	Dnd41	blood
8	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr21:40593400-40650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr21:40603200-40653400	Weak transcription	Right Atrium	heart
12	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr21:40613400-40652000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr21:40613800-40651000	Strong transcription	Fetal Thymus	thymus
15	chr21:40614000-40654400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr21:40614600-40654200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr21:40614800-40652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr21:40616400-40651800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr21:40618000-40659200	Weak transcription	Stomach Mucosa	stomach
20	chr21:40619400-40656200	Weak transcription	Ovary	ovary
21	chr21:40619600-40660200	Weak transcription	Brain Angular Gyrus	brain
22	chr21:40625000-40644000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr21:40625400-40643600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr21:40625800-40652400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr21:40626200-40653400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr21:40626800-40654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr21:40630200-40652200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr21:40630200-40661600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr21:40630200-40662800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr21:40630400-40653800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr21:40631200-40647800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr21:40631200-40663600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr21:40631600-40646600	Strong transcription	Adipose Nuclei	Adipose
34	chr21:40631600-40650600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr21:40631600-40653400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr21:40631800-40646000	Weak transcription	Small Intestine	intestine
37	chr21:40631800-40653600	Strong transcription	Fetal Intestine Large	intestine
38	chr21:40632200-40647200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr21:40632400-40643200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr21:40632600-40643400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr21:40633200-40653600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr21:40633200-40662800	Weak transcription	Esophagus	oesophagus
43	chr21:40633400-40650800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr21:40635800-40645600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr21:40635800-40653400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr21:40635800-40653600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr21:40636400-40646800	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr21:40636600-40652000	Weak transcription	Fetal Heart	heart
49	chr21:40636600-40659000	Weak transcription	Colon Smooth Muscle	Colon
50	chr21:40637000-40646000	Weak transcription	Fetal Brain Male	brain

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