Variant report

Variant	rs28360661
Chromosome Location	chr21:40681972-40681973
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40645807..40648656-chr21:40680491..40682941,2	K562	blood:
2	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
3	chr21:40645055..40648656-chr21:40680491..40684092,3	K562	blood:
4	chr21:40681416..40687854-chr21:40744378..40751195,8	K562	blood:
5	chr21:40671119..40673164-chr21:40679954..40681992,2	K562	blood:
6	chr21:40668014..40669940-chr21:40681557..40684495,2	K562	blood:

Variant related genes	Relation type
ENSG00000205581	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000238556	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1041440	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427502	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151994	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12710453	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710454	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13047663	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13047678	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13049280	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13339986	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13625	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1541102	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984022	0.84[EUR][1000 genomes]
rs2026265	0.84[EUR][1000 genomes]
rs2026267	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2150415	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2735306	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2735309	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2776307	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2776308	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2776309	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2836928	0.82[AMR][1000 genomes]
rs2836944	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836953	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836955	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836957	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836964	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836965	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836967	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836968	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836972	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836973	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836974	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836977	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2989330	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34035316	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34433511	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34578707	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672724	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34978594	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35068861	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123057	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35560196	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571600	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3945	0.83[AMR][1000 genomes]
rs55740356	0.84[AMR][1000 genomes]
rs55836299	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56306759	0.87[EUR][1000 genomes]
rs6517526	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517527	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517533	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517538	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66465538	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004583	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277978	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7282624	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283420	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283516	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283569	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354783	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128102	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128620	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128827	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8128894	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129147	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8129303	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8129355	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129416	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8130984	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133146	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8134733	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941894	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28360661	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs28360661	PSMG1	cis	Artery Tibial	GTEx
rs28360661	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs28360661	PSMG1	cis	Esophagus Mucosa	GTEx
rs28360661	HMGN1	cis	multi-tissue	Pritchard
rs28360661	PSMG1	cis	Muscle Skeletal	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	chr21:40670400-40683800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr21:40670600-40683200	Weak transcription	NHDF-Ad	bronchial
21	chr21:40671400-40683200	Weak transcription	HMEC	breast
22	chr21:40672200-40684000	Weak transcription	Aorta	Aorta
23	chr21:40672400-40683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr21:40672400-40684000	Weak transcription	Small Intestine	intestine
25	chr21:40672600-40682400	Weak transcription	Brain Anterior Caudate	brain
26	chr21:40672600-40682600	Weak transcription	Psoas Muscle	Psoas
27	chr21:40672600-40683800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr21:40672600-40684400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr21:40672800-40683400	Weak transcription	Fetal Heart	heart
30	chr21:40672800-40683800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr21:40673600-40682400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr21:40673600-40682600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr21:40673600-40682600	Weak transcription	Hela-S3	cervix
34	chr21:40673600-40683200	Weak transcription	Primary B cells from cord blood	blood
35	chr21:40673600-40683400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr21:40673600-40683600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr21:40673600-40683600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr21:40673600-40683600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr21:40673600-40683800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr21:40673600-40684000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr21:40673600-40684400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr21:40673600-40684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr21:40673800-40682600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr21:40673800-40683800	Weak transcription	Fetal Kidney	kidney
45	chr21:40675000-40683800	Weak transcription	A549	lung
46	chr21:40675400-40683400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr21:40675800-40683400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr21:40675800-40683800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr21:40675800-40684200	Weak transcription	Pancreas	Pancrea
50	chr21:40675800-40684400	Weak transcription	Gastric	stomach

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