Variant report

Variant	rs61300849
Chromosome Location	chr21:40680194-40680195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40671119..40673164-chr21:40679954..40681992,2	K562	blood:
2	chr21:40668296..40669992-chr21:40678058..40680619,2	K562	blood:
3	chr21:40678469..40680445-chr21:40759148..40760698,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1011413	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10154217	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11088471	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11088472	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11910705	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11910906	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11911822	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12626405	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1882779	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1888487	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1888488	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1963676	0.81[ASN][1000 genomes]
rs2005933	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2037925	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2142111	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2183573	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2245455	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2272576	0.85[ASN][1000 genomes]
rs2272577	0.87[ASN][1000 genomes]
rs2272578	0.87[ASN][1000 genomes]
rs2297258	0.86[ASN][1000 genomes]
rs2410123	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2410124	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836969	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836971	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836975	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836981	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836982	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836986	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836987	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836988	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34240248	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34436313	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35182074	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35769610	0.80[AFR][1000 genomes]
rs35909862	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs371625	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3746885	0.86[ASN][1000 genomes]
rs3746886	0.86[ASN][1000 genomes]
rs377098	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs414850	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs418298	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs418359	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs419469	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs428602	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs429955	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs442972	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs452377	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4624474	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4816620	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4816623	0.84[ASN][1000 genomes]
rs4817999	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4818005	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818015	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818017	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517535	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6517540	0.87[ASN][1000 genomes]
rs6517541	0.87[ASN][1000 genomes]
rs719230	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7276774	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7278985	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7279558	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7280326	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7281853	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7282604	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8127986	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8130795	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8130854	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9636957	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs997147	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9974757	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9975119	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9975562	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9978775	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9979483	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9981301	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9981656	0.84[ASN][1000 genomes]
rs9982111	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[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	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
2	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
3	esv3429298	chr21:40670131-40688774	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs61300849	PSMG1	cis	lung	GTEx
rs61300849	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs61300849	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs61300849	PSMG1	cis	Artery Tibial	GTEx
rs61300849	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	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
2	chr21:40643800-40684200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40646600-40683400	Weak transcription	Fetal Brain Male	brain
4	chr21:40655000-40683000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr21:40655400-40683200	Strong transcription	Dnd41	blood
6	chr21:40656400-40683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:40661800-40683400	Weak transcription	Stomach Mucosa	stomach
8	chr21:40663600-40683400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr21:40664000-40684200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr21:40665000-40683800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr21:40665200-40684400	Weak transcription	Colonic Mucosa	Colon
12	chr21:40666000-40682600	Weak transcription	NHLF	lung
13	chr21:40667000-40684000	Weak transcription	HSMMtube	muscle
14	chr21:40667000-40684200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr21:40669200-40684200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr21:40669400-40684000	Weak transcription	HUVEC	blood vessel
17	chr21:40669400-40684400	Weak transcription	Esophagus	oesophagus
18	chr21:40669800-40683800	Weak transcription	Brain Substantia Nigra	brain
19	chr21:40670400-40680600	Weak transcription	Brain Hippocampus Middle	brain
20	chr21:40670400-40683800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr21:40670600-40683200	Weak transcription	NHDF-Ad	bronchial
22	chr21:40671400-40683200	Weak transcription	HMEC	breast
23	chr21:40672200-40684000	Weak transcription	Aorta	Aorta
24	chr21:40672400-40683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr21:40672400-40684000	Weak transcription	Small Intestine	intestine
26	chr21:40672600-40682400	Weak transcription	Brain Anterior Caudate	brain
27	chr21:40672600-40682600	Weak transcription	Psoas Muscle	Psoas
28	chr21:40672600-40683800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr21:40672600-40684400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr21:40672800-40683400	Weak transcription	Fetal Heart	heart
31	chr21:40672800-40683800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr21:40673600-40680800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr21:40673600-40682400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr21:40673600-40682600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr21:40673600-40682600	Weak transcription	Hela-S3	cervix
36	chr21:40673600-40683200	Weak transcription	Primary B cells from cord blood	blood
37	chr21:40673600-40683400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr21:40673600-40683600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr21:40673600-40683600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr21:40673600-40683600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr21:40673600-40683800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr21:40673600-40684000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr21:40673600-40684400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr21:40673600-40684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr21:40673800-40682600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr21:40673800-40683800	Weak transcription	Fetal Kidney	kidney
47	chr21:40675000-40683800	Weak transcription	A549	lung
48	chr21:40675400-40683400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr21:40675800-40680800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr21:40675800-40683400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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