Variant report

Variant	rs10427502
Chromosome Location	chr21:40654840-40654841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	21:40653254-40655577..21:40748850-40752541	Hela-S3	cervix:
2	chr21:40654238..40657905-chr21:40719169..40721880,3	MCF-7	breast:
3	chr21:40647289..40650934-chr21:40652989..40655013,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227406	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1041440	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1065242	0.85[AMR][1000 genomes]
rs11910151	0.81[AMR][1000 genomes]
rs12151994	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12481860	0.84[AMR][1000 genomes]
rs12482181	0.81[AMR][1000 genomes]
rs12483216	0.84[AMR][1000 genomes]
rs12710453	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710454	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13047663	0.84[ASN][1000 genomes]
rs13048178	0.83[AMR][1000 genomes]
rs13049280	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13052882	0.82[AMR][1000 genomes]
rs13339986	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13625	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs14194	0.81[AMR][1000 genomes]
rs1541102	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571709	0.81[AMR][1000 genomes]
rs1984022	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2026265	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2026267	0.84[AMR][1000 genomes]
rs2150415	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2234543	0.83[AMR][1000 genomes]
rs2735306	0.84[AMR][1000 genomes]
rs2735309	0.84[AMR][1000 genomes]
rs2776307	0.84[AMR][1000 genomes]
rs2776308	0.84[AMR][1000 genomes]
rs2776309	0.84[AMR][1000 genomes]
rs28360661	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836923	0.80[AMR][1000 genomes]
rs2836925	0.84[AMR][1000 genomes]
rs2836927	0.84[AMR][1000 genomes]
rs2836929	0.83[AMR][1000 genomes]
rs2836932	0.82[AMR][1000 genomes]
rs2836933	0.86[AMR][1000 genomes]
rs2836938	0.86[AMR][1000 genomes]
rs2836944	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836953	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2836955	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836957	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836964	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836965	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836967	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836968	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836972	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836973	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836974	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836977	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34035316	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34294410	0.85[AMR][1000 genomes]
rs34433511	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34578707	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672724	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34978594	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35068861	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123057	0.84[AMR][1000 genomes]
rs35386515	0.83[AMR][1000 genomes]
rs35560196	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571600	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36113648	0.83[AMR][1000 genomes]
rs55836299	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56049536	0.86[AMR][1000 genomes]
rs56306759	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6517519	0.84[AMR][1000 genomes]
rs6517521	0.81[AMR][1000 genomes]
rs6517523	0.84[AMR][1000 genomes]
rs6517526	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517527	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517533	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517538	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66465538	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004583	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68090597	0.85[AMR][1000 genomes]
rs7277978	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7280375	0.82[AMR][1000 genomes]
rs7282624	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283420	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283516	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283569	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73221174	0.81[AMR][1000 genomes]
rs73221193	0.82[AMR][1000 genomes]
rs7354783	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127087	0.83[AMR][1000 genomes]
rs8128026	0.86[AMR][1000 genomes]
rs8128102	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128620	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128734	0.83[AMR][1000 genomes]
rs8128827	0.84[AMR][1000 genomes]
rs8128894	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129147	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8129303	0.84[AMR][1000 genomes]
rs8129355	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129416	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8130984	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8131965	0.84[AMR][1000 genomes]
rs8133146	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8134733	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941894	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10427502	PSMG1	cis	Esophagus Mucosa	GTEx
rs10427502	PSMG1	cis	lung	GTEx
rs10427502	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs10427502	PSMG1	cis	Muscle Skeletal	GTEx
rs10427502	HMGN1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:40618000-40659200	Weak transcription	Stomach Mucosa	stomach
4	chr21:40619400-40656200	Weak transcription	Ovary	ovary
5	chr21:40619600-40660200	Weak transcription	Brain Angular Gyrus	brain
6	chr21:40630200-40661600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr21:40630200-40662800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr21:40631200-40663600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr21:40633200-40662800	Weak transcription	Esophagus	oesophagus
10	chr21:40636600-40659000	Weak transcription	Colon Smooth Muscle	Colon
11	chr21:40638200-40665000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr21:40638600-40657000	Weak transcription	HMEC	breast
13	chr21:40638600-40659800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr21:40638600-40663400	Weak transcription	Gastric	stomach
15	chr21:40638600-40663400	Weak transcription	Psoas Muscle	Psoas
16	chr21:40638600-40665600	Weak transcription	Spleen	Spleen
17	chr21:40639000-40659200	Weak transcription	Brain Substantia Nigra	brain
18	chr21:40639000-40662600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr21:40639000-40663400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr21:40639200-40659600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr21:40641000-40661400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
23	chr21:40642600-40658800	Weak transcription	A549	lung
24	chr21:40642600-40659200	Weak transcription	HUVEC	blood vessel
25	chr21:40643000-40662800	Weak transcription	NHLF	lung
26	chr21:40643400-40662800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr21:40643400-40662800	Weak transcription	Brain Hippocampus Middle	brain
28	chr21:40643600-40663600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr21:40643800-40684200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr21:40646400-40656400	Weak transcription	NHEK	skin
31	chr21:40646400-40662600	Weak transcription	Small Intestine	intestine
32	chr21:40646600-40656800	Weak transcription	HSMMtube	muscle
33	chr21:40646600-40659800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr21:40646600-40662800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr21:40646600-40683400	Weak transcription	Fetal Brain Male	brain
36	chr21:40646800-40659400	Weak transcription	Colonic Mucosa	Colon
37	chr21:40647000-40658800	Weak transcription	Brain Germinal Matrix	brain
38	chr21:40647000-40659600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr21:40647200-40657200	Weak transcription	GM12878-XiMat	blood
40	chr21:40647400-40663600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr21:40650000-40659800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr21:40650200-40663400	Weak transcription	Right Ventricle	heart
43	chr21:40650200-40671600	Weak transcription	Aorta	Aorta
44	chr21:40650400-40656000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr21:40650400-40659800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr21:40650400-40659800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr21:40650600-40655800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr21:40650600-40656200	Weak transcription	Fetal Kidney	kidney
49	chr21:40650600-40656400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr21:40650600-40657000	Weak transcription	Brain Anterior Caudate	brain

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