Variant report

Variant	rs13049280
Chromosome Location	chr21:40594656-40594657
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40585420..40588225-chr21:40594094..40595932,2	K562	blood:
2	chr21:40560351..40562660-chr21:40594033..40595744,3	K562	blood:
3	chr21:40589784..40591764-chr21:40593259..40594916,2	K562	blood:
4	chr21:40566697..40568656-chr21:40592903..40594703,2	MCF-7	breast:
5	chr21:40592475..40595061-chr21:40604619..40606247,2	MCF-7	breast:
6	chr21:40590457..40592337-chr21:40593450..40595076,2	MCF-7	breast:
7	chr21:40587436..40591443-chr21:40593208..40596676,4	MCF-7	breast:
8	chr21:40592170..40594863-chr21:40595733..40597687,2	K562	blood:
9	chr21:40592903..40594830-chr21:40600415..40602251,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction
ENSG00000232608	Chromatin interaction
ENSG00000237373	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1041440	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10427502	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1065242	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11910151	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11911112	0.85[EUR][1000 genomes]
rs11911149	0.85[EUR][1000 genomes]
rs12151994	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12481860	0.89[EUR][1000 genomes]
rs12482156	0.83[EUR][1000 genomes]
rs12482181	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12482857	0.83[EUR][1000 genomes]
rs12483216	0.89[EUR][1000 genomes]
rs12710453	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12710454	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13047550	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13047663	0.81[AMR][1000 genomes]
rs13048178	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13052882	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13339986	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13625	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs14194	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1541102	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1571709	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1984022	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026265	0.96[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026267	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2150415	0.85[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2234543	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2249651	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2735306	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2776307	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2776309	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28360661	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836920	1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2836921	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836923	0.85[EUR][1000 genomes]
rs2836924	0.85[EUR][1000 genomes]
rs2836925	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836927	0.89[EUR][1000 genomes]
rs2836928	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836929	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836932	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836938	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836939	0.85[YRI][hapmap]
rs2836944	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836953	0.92[EUR][1000 genomes]
rs2836955	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836957	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836964	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836965	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836967	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836968	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836972	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836973	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836974	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2836977	0.88[EUR][1000 genomes]
rs34035316	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34176878	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34294410	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34394827	0.85[EUR][1000 genomes]
rs34433511	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478864	0.82[EUR][1000 genomes]
rs34578707	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34592564	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34672724	0.88[EUR][1000 genomes]
rs34978594	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35064900	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35068861	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35386515	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35391055	0.85[EUR][1000 genomes]
rs35560196	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35571600	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35774464	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36113648	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3945	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]
rs4817996	0.85[EUR][1000 genomes]
rs55836299	0.89[EUR][1000 genomes]
rs56306759	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517513	0.85[EUR][1000 genomes]
rs6517514	0.85[EUR][1000 genomes]
rs6517519	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6517521	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6517523	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517526	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517527	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517533	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517538	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66465538	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68004583	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68090597	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71184665	0.88[EUR][1000 genomes]
rs7277978	0.85[ASN][1000 genomes]
rs7280375	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7282624	0.88[EUR][1000 genomes]
rs7283420	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7283516	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7283569	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73221174	0.81[EUR][1000 genomes]
rs73221193	0.88[EUR][1000 genomes]
rs7354783	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8127087	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8128026	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8128102	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128191	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8128620	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128734	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128894	0.85[EUR][1000 genomes]
rs8129147	0.84[EUR][1000 genomes]
rs8129355	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129416	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8130556	0.82[EUR][1000 genomes]
rs8130984	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8131965	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8132285	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8132295	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8132333	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8132419	0.85[EUR][1000 genomes]
rs8132568	0.85[EUR][1000 genomes]
rs8133146	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8134733	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9941894	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13049280	PSMG1	cis	lung	GTEx
rs13049280	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs13049280	PSMG1	cis	Muscle Skeletal	GTEx
rs13049280	PSMG1	cis	Nerve Tibial	GTEx
rs13049280	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs13049280	DSCR2	cis	normal skin	skin_eQTL
rs13049280	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	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
3	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr21:40565400-40653600	Strong transcription	Dnd41	blood
13	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:40571400-40602400	Weak transcription	Fetal Brain Male	brain
18	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
19	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
20	chr21:40576200-40597400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr21:40577200-40595400	Weak transcription	Colonic Mucosa	Colon
22	chr21:40577600-40596000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr21:40577800-40598800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr21:40578000-40595600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr21:40578000-40598800	Weak transcription	Gastric	stomach
26	chr21:40578000-40607600	Weak transcription	Aorta	Aorta
27	chr21:40578600-40595400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr21:40578600-40595400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr21:40578600-40608000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr21:40578800-40606600	Weak transcription	Brain Substantia Nigra	brain
31	chr21:40579000-40598800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr21:40580400-40606400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr21:40580600-40607600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:40580800-40607200	Weak transcription	Spleen	Spleen
35	chr21:40581200-40595400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr21:40581800-40607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr21:40582200-40614200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr21:40582400-40597400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr21:40582400-40598600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr21:40582600-40602000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr21:40582600-40622000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr21:40583600-40606800	Weak transcription	NHLF	lung
45	chr21:40584200-40598200	Weak transcription	HepG2	liver
46	chr21:40586600-40597000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr21:40586600-40597000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr21:40586600-40599200	Weak transcription	Hela-S3	cervix
49	chr21:40587400-40595400	Weak transcription	Brain Angular Gyrus	brain
50	chr21:40587800-40598200	Weak transcription	Brain Germinal Matrix	brain

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