Variant report

Variant	rs3945
Chromosome Location	chr21:40566067-40566068
allele	A/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	chr21:40564655..40567110-chr21:40569434..40571576,2	MCF-7	breast:
4	chr21:40560024..40562284-chr21:40564214..40567219,3	MCF-7	breast:
5	chr21:40564573..40566805-chr21:40573736..40576146,2	K562	blood:

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

Extended variants
information (count: 115 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1041440	0.84[EUR][1000 genomes]
rs1065242	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11910151	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11911112	0.94[EUR][1000 genomes]
rs11911149	0.94[EUR][1000 genomes]
rs12481860	0.98[EUR][1000 genomes]
rs12482156	0.92[EUR][1000 genomes]
rs12482181	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12482857	0.92[EUR][1000 genomes]
rs12483216	0.98[EUR][1000 genomes]
rs12710453	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710454	0.82[AMR][1000 genomes]
rs13047550	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13047663	0.81[AMR][1000 genomes]
rs13048178	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13049280	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13052882	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13339986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs14194	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1541102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1571709	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1984022	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2026265	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2026267	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2150415	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2234543	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249651	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2735306	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2776307	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2776309	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28360661	0.83[AMR][1000 genomes]
rs2836920	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2836921	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836923	0.94[EUR][1000 genomes]
rs2836924	0.94[EUR][1000 genomes]
rs2836925	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2836927	0.98[EUR][1000 genomes]
rs2836928	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2836929	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2836932	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2836933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836938	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836939	1.00[YRI][hapmap]
rs2836944	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836953	0.84[EUR][1000 genomes]
rs2836955	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836957	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836965	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2836967	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2836968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2836972	0.84[EUR][1000 genomes]
rs2836973	0.84[EUR][1000 genomes]
rs2836974	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34035316	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34176878	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34294410	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34394827	0.94[EUR][1000 genomes]
rs34433511	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34478864	0.91[EUR][1000 genomes]
rs34578707	0.83[AMR][1000 genomes]
rs34592564	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34978594	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35064900	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35068861	0.83[EUR][1000 genomes]
rs35386515	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35391055	0.94[EUR][1000 genomes]
rs35571600	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36113648	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4817996	0.94[EUR][1000 genomes]
rs55836299	0.81[EUR][1000 genomes]
rs56049536	0.87[EUR][1000 genomes]
rs56112725	0.82[EUR][1000 genomes]
rs56306759	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6517513	0.94[EUR][1000 genomes]
rs6517514	0.94[EUR][1000 genomes]
rs6517519	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs6517521	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6517523	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517526	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517527	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517533	0.84[EUR][1000 genomes]
rs6517538	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs66465538	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs68004583	0.81[EUR][1000 genomes]
rs68090597	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71184665	0.96[EUR][1000 genomes]
rs7280375	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7283420	0.83[AMR][1000 genomes]
rs7283516	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7283569	0.84[EUR][1000 genomes]
rs73221174	0.90[EUR][1000 genomes]
rs73221193	0.96[EUR][1000 genomes]
rs7354783	0.84[EUR][1000 genomes]
rs8127087	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8128026	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8128102	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128191	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs8128734	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129355	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129416	0.85[EUR][1000 genomes]
rs8130556	0.91[EUR][1000 genomes]
rs8130984	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs8131965	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8132295	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs8132333	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs8132419	0.94[EUR][1000 genomes]
rs8132568	0.94[EUR][1000 genomes]
rs8133146	0.87[EUR][1000 genomes]
rs9941894	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3945	PSMG1	cis	Esophagus Mucosa	GTEx
rs3945	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs3945	DSCR2	cis	normal skin	skin_eQTL
rs3945	PSMG1	cis	Nerve Tibial	GTEx
rs3945	PSMG1	cis	lung	GTEx
rs3945	PSMG1	cis	Muscle Skeletal	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	chr21:40556600-40566400	Weak transcription	Fetal Muscle Leg	muscle
16	chr21:40556600-40566600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr21:40556600-40566800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr21:40556600-40567400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr21:40556600-40568200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr21:40556600-40568200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr21:40556600-40568200	Weak transcription	Brain Angular Gyrus	brain
22	chr21:40556600-40568200	Weak transcription	Brain Germinal Matrix	brain
23	chr21:40556600-40568200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr21:40556600-40568200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr21:40556600-40568400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr21:40556600-40568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr21:40556600-40568800	Weak transcription	Aorta	Aorta
28	chr21:40556600-40570400	Weak transcription	Colonic Mucosa	Colon
29	chr21:40556600-40571000	Weak transcription	Fetal Stomach	stomach
30	chr21:40556600-40576600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr21:40556800-40566200	Weak transcription	Primary B cells from cord blood	blood
32	chr21:40556800-40566200	Weak transcription	Brain Anterior Caudate	brain
33	chr21:40556800-40566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr21:40556800-40566400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr21:40556800-40567600	Weak transcription	Primary T cells from cord blood	blood
36	chr21:40556800-40567600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr21:40556800-40567600	Weak transcription	Fetal Brain Male	brain
38	chr21:40556800-40567600	Weak transcription	HepG2	liver
39	chr21:40556800-40567800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr21:40556800-40567800	Weak transcription	Fetal Kidney	kidney
41	chr21:40556800-40568200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr21:40556800-40568400	Weak transcription	Fetal Heart	heart
43	chr21:40557000-40566200	Weak transcription	Adipose Nuclei	Adipose
44	chr21:40557000-40566400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr21:40557000-40566400	Weak transcription	Fetal Lung	lung
46	chr21:40557000-40566400	Weak transcription	HUVEC	blood vessel
47	chr21:40557000-40567800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr21:40557000-40567800	Weak transcription	Brain Substantia Nigra	brain
49	chr21:40557000-40568600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr21:40557000-40570600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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