Variant report

Variant	rs35909862
Chromosome Location	chr21:40621158-40621159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1011413	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10154217	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11088471	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11088472	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11702268	0.87[ASN][1000 genomes]
rs11910705	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11910906	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11910971	0.87[ASN][1000 genomes]
rs11911822	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12626405	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1541100	0.86[ASN][1000 genomes]
rs1541101	0.86[ASN][1000 genomes]
rs1882779	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1888487	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1888488	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1984748	0.84[ASN][1000 genomes]
rs2005933	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2026266	0.87[ASN][1000 genomes]
rs2037925	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2142111	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2142117	0.84[ASN][1000 genomes]
rs2183573	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2183574	0.87[ASN][1000 genomes]
rs2183575	0.87[ASN][1000 genomes]
rs2183576	0.87[ASN][1000 genomes]
rs2245455	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2410121	0.86[ASN][1000 genomes]
rs2410123	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2410124	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836971	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836975	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836981	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2836982	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836986	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836987	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836988	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34240248	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34436313	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35182074	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs371625	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs377098	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs414850	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs418298	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs418359	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs419469	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs428602	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs429955	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs442972	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs452377	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4624474	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4816619	0.87[ASN][1000 genomes]
rs4816620	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4817999	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4818004	0.85[ASN][1000 genomes]
rs4818005	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818006	0.87[ASN][1000 genomes]
rs4818007	0.87[ASN][1000 genomes]
rs4818011	0.85[ASN][1000 genomes]
rs4818012	0.84[ASN][1000 genomes]
rs4818014	0.81[ASN][1000 genomes]
rs4818015	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4818017	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59916147	0.81[AFR][1000 genomes]
rs61300849	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6517529	0.85[ASN][1000 genomes]
rs6517530	0.87[ASN][1000 genomes]
rs6517531	0.86[ASN][1000 genomes]
rs6517532	0.86[ASN][1000 genomes]
rs6517534	0.83[ASN][1000 genomes]
rs6517535	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517536	0.86[ASN][1000 genomes]
rs6517537	0.86[ASN][1000 genomes]
rs6517539	0.85[ASN][1000 genomes]
rs718225	0.86[ASN][1000 genomes]
rs719230	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7275773	0.85[ASN][1000 genomes]
rs7276559	0.85[ASN][1000 genomes]
rs7276698	0.85[ASN][1000 genomes]
rs7276774	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7278985	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7279558	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7280149	0.87[ASN][1000 genomes]
rs7280326	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7281853	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7282604	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7282724	0.85[ASN][1000 genomes]
rs7282947	0.87[ASN][1000 genomes]
rs7283439	0.85[ASN][1000 genomes]
rs7283652	0.85[ASN][1000 genomes]
rs8127391	0.86[ASN][1000 genomes]
rs8127986	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8128118	0.87[ASN][1000 genomes]
rs8129847	0.87[ASN][1000 genomes]
rs8130099	0.83[ASN][1000 genomes]
rs8130774	0.85[ASN][1000 genomes]
rs8130795	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8130854	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8131091	0.86[ASN][1000 genomes]
rs8131150	0.83[ASN][1000 genomes]
rs8131263	0.87[ASN][1000 genomes]
rs8131307	0.81[ASN][1000 genomes]
rs8132230	0.85[ASN][1000 genomes]
rs914157	0.87[ASN][1000 genomes]
rs9636957	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs971229	0.86[ASN][1000 genomes]
rs973521	0.86[ASN][1000 genomes]
rs997147	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9974757	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9975119	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9975562	0.87[EUR][1000 genomes]
rs9977762	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9978591	0.87[ASN][1000 genomes]
rs9978775	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9978953	0.83[ASN][1000 genomes]
rs9979483	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9979547	0.81[ASN][1000 genomes]
rs9981301	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9982111	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv587481	chr21:40598721-40627020	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs35909862	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs35909862	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs35909862	PSMG1	cis	lung	GTEx
rs35909862	PSMG1	cis	Artery Tibial	GTEx
rs35909862	PSMG1	cis	Nerve Tibial	GTEx
rs35909862	PSMG1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
2	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr21:40565400-40653600	Strong transcription	Dnd41	blood
9	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
11	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
12	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr21:40582600-40622000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr21:40591200-40621600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr21:40591200-40622200	Strong transcription	Liver	Liver
17	chr21:40591400-40625200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr21:40592000-40622400	Strong transcription	K562	blood
19	chr21:40593400-40650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr21:40595800-40624000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr21:40597200-40635600	Weak transcription	Fetal Heart	heart
22	chr21:40598200-40629800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr21:40598600-40625000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr21:40599200-40623800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr21:40603000-40627800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr21:40603200-40653400	Weak transcription	Right Atrium	heart
27	chr21:40608400-40628400	Weak transcription	Lung	lung
28	chr21:40608400-40632200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr21:40608400-40632600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr21:40608400-40634200	Weak transcription	NHLF	lung
31	chr21:40608400-40638200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr21:40608600-40627000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:40608600-40628400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr21:40608600-40636400	Weak transcription	Aorta	Aorta
36	chr21:40608800-40623600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr21:40608800-40627200	Weak transcription	Esophagus	oesophagus
38	chr21:40609200-40623000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr21:40609200-40623400	Weak transcription	Colon Smooth Muscle	Colon
40	chr21:40609200-40627600	Weak transcription	Right Ventricle	heart
41	chr21:40609800-40635400	Weak transcription	Fetal Brain Male	brain
42	chr21:40610800-40626400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr21:40612200-40628600	Weak transcription	Brain Anterior Caudate	brain
44	chr21:40612800-40621200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr21:40613400-40622200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr21:40613400-40652000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr21:40613600-40621200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr21:40613600-40621600	Strong transcription	Primary B cells from cord blood	blood
49	chr21:40613600-40622400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr21:40613800-40651000	Strong transcription	Fetal Thymus	thymus

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