Variant report

Variant	rs1984022
Chromosome Location	chr21:40596085-40596086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40595422..40597101-chr21:40606197..40608970,2	K562	blood:
2	chr21:40592170..40594863-chr21:40595733..40597687,2	K562	blood:
3	chr21:40587436..40591443-chr21:40593208..40596676,4	MCF-7	breast:
4	21:40595367-40598507..21:40748850-40752541	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction
ENSG00000232608	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000229623	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1041440	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10427502	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1065242	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11088471	0.91[YRI][hapmap]
rs11910151	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11911112	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11911149	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12151994	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12481860	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12482156	0.83[EUR][1000 genomes]
rs12482181	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12482857	0.83[EUR][1000 genomes]
rs12483216	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12710453	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710454	0.88[EUR][1000 genomes]
rs13047550	0.84[EUR][1000 genomes]
rs13048178	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13049280	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13052882	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13339986	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13625	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs14194	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1541102	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1571709	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1888488	0.86[YRI][hapmap]
rs2026265	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026267	0.90[CEU][hapmap]
rs2037925	0.86[YRI][hapmap]
rs2142111	0.83[YRI][hapmap]
rs2150413	0.89[YRI][hapmap]
rs2150414	0.89[YRI][hapmap]
rs2150415	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2234543	0.95[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2245455	0.81[YRI][hapmap]
rs2410106	0.83[AMR][1000 genomes]
rs2410123	0.96[YRI][hapmap]
rs2735306	0.90[CEU][hapmap]
rs2776307	0.90[CEU][hapmap]
rs2776309	0.90[CEU][hapmap]
rs28360661	0.84[EUR][1000 genomes]
rs2836920	0.82[CEU][hapmap]
rs2836921	0.84[EUR][1000 genomes]
rs2836923	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836924	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836925	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836927	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836928	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836929	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836932	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836933	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836938	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836944	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836953	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836955	0.95[CEU][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836956	0.89[YRI][hapmap]
rs2836957	0.95[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836958	0.89[YRI][hapmap]
rs2836964	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2836965	0.95[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836967	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836968	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2836972	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836973	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836974	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836977	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2836981	0.85[YRI][hapmap]
rs2836982	0.85[YRI][hapmap]
rs2836986	0.93[YRI][hapmap]
rs2836987	0.96[YRI][hapmap]
rs2836988	0.86[YRI][hapmap]
rs34035316	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34176878	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34294410	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34394827	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34433511	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34478864	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34578707	0.85[EUR][1000 genomes]
rs34592564	0.84[EUR][1000 genomes]
rs34672724	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34978594	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35064900	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35068861	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35386515	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35391055	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35560196	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35571600	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36113648	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3945	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs428602	0.90[YRI][hapmap]
rs4624474	0.86[YRI][hapmap]
rs4817996	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55836299	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56049536	0.86[AMR][1000 genomes]
rs56112725	0.81[AMR][1000 genomes]
rs56306759	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517513	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6517514	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6517519	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6517521	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6517523	0.95[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6517526	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517527	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517533	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6517538	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66465538	0.92[EUR][1000 genomes]
rs68004583	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs68090597	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71184665	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7277978	0.81[AMR][1000 genomes]
rs7278297	0.90[YRI][hapmap]
rs7280375	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7281853	0.85[YRI][hapmap]
rs7282624	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7283420	0.87[EUR][1000 genomes]
rs7283516	0.95[CEU][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7283569	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73221174	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73221193	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7354783	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8127087	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8128026	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8128102	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128191	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8128620	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8128734	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8128894	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8129147	0.84[EUR][1000 genomes]
rs8129355	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129416	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8130556	0.82[EUR][1000 genomes]
rs8130984	0.95[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8131965	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8132285	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs8132295	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8132333	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8132419	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8132568	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8133146	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8134733	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9941894	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs9981301	0.86[YRI][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1984022	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs1984022	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs1984022	PSMG1	cis	Artery Tibial	GTEx
rs1984022	DSCR2	cis	normal skin	skin_eQTL
rs1984022	PSMG1	cis	Nerve Tibial	GTEx
rs1984022	DSCR2	cis	uninvolved skin	skin_eQTL
rs1984022	PSMG1	cis	Esophagus Mucosa	GTEx
rs1984022	PSMG1	cis	lung	GTEx
rs1984022	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	chr21:40556200-40602600	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	chr21:40577800-40598800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr21:40578000-40598800	Weak transcription	Gastric	stomach
23	chr21:40578000-40607600	Weak transcription	Aorta	Aorta
24	chr21:40578600-40608000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr21:40578800-40606600	Weak transcription	Brain Substantia Nigra	brain
26	chr21:40579000-40598800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr21:40580400-40606400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr21:40580600-40607600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr21:40580800-40607200	Weak transcription	Spleen	Spleen
30	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr21:40581800-40607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr21:40582200-40614200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr21:40582400-40597400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr21:40582400-40598600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr21:40582600-40602000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr21:40582600-40622000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr21:40583600-40606800	Weak transcription	NHLF	lung
39	chr21:40584200-40598200	Weak transcription	HepG2	liver
40	chr21:40586600-40597000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr21:40586600-40597000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr21:40586600-40599200	Weak transcription	Hela-S3	cervix
43	chr21:40587800-40598200	Weak transcription	Brain Germinal Matrix	brain
44	chr21:40587800-40599800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr21:40588000-40599600	Weak transcription	Esophagus	oesophagus
46	chr21:40588000-40601800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr21:40588600-40598600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr21:40588800-40607800	Weak transcription	Right Ventricle	heart
49	chr21:40589600-40598600	Weak transcription	Brain Anterior Caudate	brain
50	chr21:40589600-40598800	Weak transcription	Lung	lung

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