Variant report

Variant	rs34978594
Chromosome Location	chr21:40580003-40580004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40579156..40581832-chr21:40603360..40605633,2	K562	blood:
2	chr21:40578990..40581803-chr21:40609609..40612432,2	K562	blood:
3	chr21:40574761..40577366-chr21:40579952..40583653,3	MCF-7	breast:
4	chr21:40574695..40577813-chr21:40579621..40584653,4	K562	blood:
5	chr21:40578179..40580056-chr21:40585515..40588059,2	K562	blood:
6	chr21:40579851..40582767-chr21:40583225..40585456,3	K562	blood:

Extended variants
information (count: 120 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1041440	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10427502	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1065242	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11910151	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11911112	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11911149	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12151994	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12481860	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12482156	0.83[EUR][1000 genomes]
rs12482181	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12482857	0.83[EUR][1000 genomes]
rs12483216	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12710453	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12710454	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13047550	0.84[EUR][1000 genomes]
rs13048178	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13049280	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13052882	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13339986	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13625	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs14194	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1541102	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1571709	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1984022	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026265	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2150415	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2234543	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2410106	0.86[AMR][1000 genomes]
rs28360661	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836921	0.84[EUR][1000 genomes]
rs2836923	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836924	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836925	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836927	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836928	0.89[EUR][1000 genomes]
rs2836929	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836932	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836933	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836938	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836944	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836953	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836955	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836957	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836964	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836965	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836967	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836968	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836972	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836973	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836974	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836977	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34035316	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34176878	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34294410	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34394827	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34433511	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478864	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34578707	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34592564	0.84[EUR][1000 genomes]
rs34672724	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35064900	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35068861	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35386515	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35391055	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35560196	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35571600	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35774464	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36113648	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3945	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4817996	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55836299	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56049536	0.83[AMR][1000 genomes]
rs56306759	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517513	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6517514	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6517519	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6517521	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6517523	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517533	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517538	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66465538	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68004583	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68090597	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71184665	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7277978	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7280375	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7282624	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7283420	0.85[EUR][1000 genomes]
rs7283516	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7283569	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73221174	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73221193	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7354783	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8127087	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8128026	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8128102	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128191	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8128620	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128734	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128894	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8129147	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8129355	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129416	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8130556	0.84[EUR][1000 genomes]
rs8130984	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8131965	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8132295	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8132333	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8132419	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8132568	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8133146	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8134733	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9941894	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs34978594	PSMG1	cis	Esophagus Mucosa	GTEx
rs34978594	PSMG1	cis	Muscle Skeletal	GTEx
rs34978594	PSMG1	cis	Artery Tibial	GTEx
rs34978594	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs34978594	HMGN1	cis	multi-tissue	Pritchard
rs34978594	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs34978594	PSMG1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
3	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr21:40563200-40581000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:40563600-40588600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr21:40564800-40587800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr21:40565000-40581200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr21:40565000-40592600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr21:40565400-40580800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr21:40565400-40653600	Strong transcription	Dnd41	blood
19	chr21:40565600-40585600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr21:40565600-40590200	Strong transcription	Liver	Liver
21	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr21:40565800-40580600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr21:40565800-40581400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr21:40565800-40590600	Strong transcription	Fetal Thymus	thymus
25	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr21:40566200-40590600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr21:40566200-40590600	Strong transcription	Adipose Nuclei	Adipose
28	chr21:40566400-40580200	Strong transcription	K562	blood
29	chr21:40566400-40580800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr21:40566600-40581200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr21:40567400-40585400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr21:40567400-40592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr21:40567600-40580600	Strong transcription	GM12878-XiMat	blood
35	chr21:40567600-40581000	Strong transcription	Primary T cells from cord blood	blood
36	chr21:40567600-40581200	Strong transcription	Fetal Muscle Leg	muscle
37	chr21:40567600-40583800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr21:40567600-40585000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr21:40568200-40581400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr21:40568200-40584600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr21:40568400-40580600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr21:40569000-40581600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr21:40569400-40580200	Strong transcription	Fetal Intestine Large	intestine
44	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr21:40570000-40581200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr21:40570600-40589800	Weak transcription	Stomach Mucosa	stomach
47	chr21:40571400-40602400	Weak transcription	Fetal Brain Male	brain
48	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
49	chr21:40573000-40580400	Strong transcription	Brain Anterior Caudate	brain
50	chr21:40573400-40583600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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