Variant report

Variant	rs35571600
Chromosome Location	chr21:40590624-40590625
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	IRF1	chr21:40590575-40590637	K562	blood:	n/a	n/a
2	POLR2A	chr21:40589924-40590655	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40554637..40556936-chr21:40588612..40590641,2	K562	blood:
2	21:40583765-40590917..21:40718004-40719183	GM12878	blood:
3	21:40583765-40590917..21:40796857-40798340	Hela-S3	cervix:

Variant related genes	Relation type
BRWD1	TF binding region
ENSG00000272991	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000205581	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1041440	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10427502	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1065242	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11910151	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11911112	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11911149	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12151994	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12481860	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12482156	0.82[EUR][1000 genomes]
rs12482181	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12482857	0.82[EUR][1000 genomes]
rs12483216	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12710453	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12710454	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13047550	0.83[EUR][1000 genomes]
rs13048178	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13049280	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13052882	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13339986	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13625	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs14194	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1541102	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1571709	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1984022	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026265	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2150415	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2234543	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2410106	0.86[AMR][1000 genomes]
rs28360661	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836921	0.83[EUR][1000 genomes]
rs2836923	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836924	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836925	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2836927	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2836928	0.88[EUR][1000 genomes]
rs2836929	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836932	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836933	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836938	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836944	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836953	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836955	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836957	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836964	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836965	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836967	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836968	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836972	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836973	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836974	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836977	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34035316	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34176878	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34294410	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34394827	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34433511	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478864	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34578707	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34592564	0.83[EUR][1000 genomes]
rs34672724	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34978594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35064900	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35068861	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35386515	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35391055	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35560196	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36113648	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3945	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4817996	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55836299	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56049536	0.83[AMR][1000 genomes]
rs56306759	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517513	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6517514	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6517519	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6517521	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6517523	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517526	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517533	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517538	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66465538	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68004583	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68090597	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71184665	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7277978	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7280375	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7282624	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7283420	0.86[EUR][1000 genomes]
rs7283516	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7283569	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73221174	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73221193	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7354783	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8127087	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8128026	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8128102	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128191	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8128620	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128734	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128894	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8129147	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8129355	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129416	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8130556	0.83[EUR][1000 genomes]
rs8130984	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8131965	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8132295	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8132333	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8132419	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8132568	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8133146	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8134733	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9941894	0.91[EUR][1000 genomes];0.89[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs35571600	PSMG1	cis	Muscle Skeletal	GTEx
rs35571600	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs35571600	PSMG1	cis	lung	GTEx
rs35571600	PSMG1	cis	Artery Tibial	GTEx
rs35571600	PSMG1	cis	Esophagus Mucosa	GTEx
rs35571600	HMGN1	cis	multi-tissue	Pritchard
rs35571600	PSMG1	cis	Skin Sun Exposed Lower leg	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	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr21:40565000-40592600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr21:40565400-40653600	Strong transcription	Dnd41	blood
14	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr21:40567400-40592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr21:40571400-40602400	Weak transcription	Fetal Brain Male	brain
20	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
21	chr21:40573800-40593600	Weak transcription	A549	lung
22	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
23	chr21:40576200-40597400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr21:40576400-40592400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr21:40576800-40593600	Weak transcription	Right Atrium	heart
26	chr21:40577200-40593800	Weak transcription	Colon Smooth Muscle	Colon
27	chr21:40577200-40595400	Weak transcription	Colonic Mucosa	Colon
28	chr21:40577600-40596000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr21:40577800-40598800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr21:40578000-40595600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr21:40578000-40598800	Weak transcription	Gastric	stomach
32	chr21:40578000-40607600	Weak transcription	Aorta	Aorta
33	chr21:40578600-40595400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr21:40578600-40595400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr21:40578600-40608000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr21:40578800-40606600	Weak transcription	Brain Substantia Nigra	brain
37	chr21:40579000-40598800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr21:40580400-40591600	Weak transcription	Fetal Heart	heart
39	chr21:40580400-40606400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr21:40580600-40592600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr21:40580600-40607600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr21:40580800-40607200	Weak transcription	Spleen	Spleen
43	chr21:40581200-40593600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr21:40581200-40595400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr21:40581800-40607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr21:40582200-40614200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr21:40582400-40597400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr21:40582400-40598600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr21:40582600-40591600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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