Variant report

Variant	rs1065242
Chromosome Location	chr21:40567716-40567717
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40551398..40560769-chr21:40565658..40576445,18	K562	blood:
2	21:40565363-40575691..21:40718004-40719183	GM12878	blood:
3	chr21:40566344..40569096-chr21:40684027..40685984,2	MCF-7	breast:
4	chr21:40566697..40568656-chr21:40592903..40594703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205581	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000272991	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1041440	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10427502	0.85[AMR][1000 genomes]
rs11910151	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11911112	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11911149	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12151994	0.82[AMR][1000 genomes]
rs12481860	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12482156	0.90[EUR][1000 genomes]
rs12482181	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12482857	0.90[EUR][1000 genomes]
rs12483216	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12710453	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710454	0.80[EUR][1000 genomes]
rs13047550	0.91[EUR][1000 genomes]
rs13048178	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13049280	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13052882	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13339986	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13625	0.86[AMR][1000 genomes]
rs14194	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1541102	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1571709	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1984022	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2026265	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2150415	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2234543	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410106	0.84[AMR][1000 genomes]
rs2836921	0.91[EUR][1000 genomes]
rs2836923	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2836924	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2836925	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836927	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836928	0.96[EUR][1000 genomes]
rs2836929	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2836932	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2836933	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836938	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836944	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836953	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836955	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836957	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836964	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836965	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836967	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836968	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836972	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2836973	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2836974	0.84[AMR][1000 genomes]
rs2836977	0.86[AMR][1000 genomes]
rs34035316	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34176878	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34294410	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34394827	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34433511	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34478864	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34592564	0.91[EUR][1000 genomes]
rs34672724	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34978594	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35064900	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35068861	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35386515	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35391055	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35560196	0.86[AMR][1000 genomes]
rs35571600	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36113648	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3945	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4817996	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55836299	0.86[AMR][1000 genomes]
rs56049536	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56112725	0.81[EUR][1000 genomes]
rs56306759	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6517513	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6517514	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6517519	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6517521	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6517523	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517526	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517527	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517533	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6517538	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66465538	0.83[EUR][1000 genomes]
rs68004583	0.85[AMR][1000 genomes]
rs68090597	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71184665	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7277978	0.82[AMR][1000 genomes]
rs7280375	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7282624	0.86[AMR][1000 genomes]
rs7283516	0.82[AMR][1000 genomes]
rs7283569	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73221174	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73221193	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7354783	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8127087	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8128026	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8128102	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128191	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8128620	0.86[AMR][1000 genomes]
rs8128734	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128894	0.86[AMR][1000 genomes]
rs8129355	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129416	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8130556	0.91[EUR][1000 genomes]
rs8130984	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8131965	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132295	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8132333	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8132419	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8132568	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8133146	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8134733	0.84[AMR][1000 genomes]
rs9941894	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1065242	PSMG1	cis	Artery Tibial	GTEx
rs1065242	PSMG1	cis	lung	GTEx
rs1065242	PSMG1	cis	Esophagus Mucosa	GTEx
rs1065242	PSMG1	cis	Muscle Skeletal	GTEx
rs1065242	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40567800	Weak transcription	Left Ventricle	heart
2	chr21:40556200-40568600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr21:40556200-40568800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:40556200-40570200	Weak transcription	Stomach Mucosa	stomach
5	chr21:40556200-40570800	Weak transcription	Small Intestine	intestine
6	chr21:40556200-40571000	Weak transcription	Lung	lung
7	chr21:40556200-40571200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:40556200-40576600	Weak transcription	Esophagus	oesophagus
9	chr21:40556200-40576600	Weak transcription	Pancreas	Pancrea
10	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr21:40556400-40568400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr21:40556400-40568400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr21:40556400-40568800	Weak transcription	Psoas Muscle	Psoas
14	chr21:40556400-40571000	Weak transcription	Ovary	ovary
15	chr21:40556600-40568200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr21:40556600-40568200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr21:40556600-40568200	Weak transcription	Brain Angular Gyrus	brain
18	chr21:40556600-40568200	Weak transcription	Brain Germinal Matrix	brain
19	chr21:40556600-40568200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr21:40556600-40568200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr21:40556600-40568400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr21:40556600-40568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr21:40556600-40568800	Weak transcription	Aorta	Aorta
24	chr21:40556600-40570400	Weak transcription	Colonic Mucosa	Colon
25	chr21:40556600-40571000	Weak transcription	Fetal Stomach	stomach
26	chr21:40556600-40576600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr21:40556800-40567800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr21:40556800-40567800	Weak transcription	Fetal Kidney	kidney
29	chr21:40556800-40568200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr21:40556800-40568400	Weak transcription	Fetal Heart	heart
31	chr21:40557000-40567800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr21:40557000-40567800	Weak transcription	Brain Substantia Nigra	brain
33	chr21:40557000-40568600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr21:40557000-40570600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr21:40557200-40567800	Weak transcription	A549	lung
36	chr21:40557200-40569400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr21:40559000-40568600	Weak transcription	Colon Smooth Muscle	Colon
38	chr21:40559200-40568600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr21:40560400-40570800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr21:40561000-40568200	Weak transcription	HSMMtube	muscle
41	chr21:40562400-40568200	Weak transcription	Thymus	Thymus
42	chr21:40562600-40567800	Weak transcription	HMEC	breast
43	chr21:40562600-40568200	Weak transcription	Right Ventricle	heart
44	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
45	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr21:40563200-40568600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr21:40563200-40581000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr21:40563400-40567800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr21:40563400-40569000	Weak transcription	NHLF	lung
50	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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