Variant report

Variant	rs9976530
Chromosome Location	chr21:47910659-47910660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47903644..47905346-chr21:47909530..47912151,2	MCF-7	breast:
2	chr21:47877136..47880459-chr21:47909304..47911302,3	K562	blood:

Variant related genes	Relation type
ENSG00000160305	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1007893	0.90[ASN][1000 genomes]
rs1008548	0.82[ASN][1000 genomes]
rs1008549	0.82[ASN][1000 genomes]
rs1029231	0.86[ASN][1000 genomes]
rs10775681	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10854484	0.81[ASN][1000 genomes]
rs11089070	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11700510	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11700596	0.87[ASN][1000 genomes]
rs11701310	0.86[ASN][1000 genomes]
rs11701569	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11701571	0.85[ASN][1000 genomes]
rs11701815	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11701902	0.88[ASN][1000 genomes]
rs11702190	0.82[ASN][1000 genomes]
rs11702278	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11702701	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11702704	0.86[ASN][1000 genomes]
rs11702718	0.90[ASN][1000 genomes]
rs11702822	0.81[ASN][1000 genomes]
rs12627084	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1892691	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1892692	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2070432	0.86[ASN][1000 genomes]
rs2070433	0.86[ASN][1000 genomes]
rs2070435	0.86[ASN][1000 genomes]
rs2073380	0.84[ASN][1000 genomes]
rs2096507	0.91[ASN][1000 genomes]
rs2236616	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2268524	0.84[ASN][1000 genomes]
rs2300561	0.87[ASN][1000 genomes]
rs2300562	0.91[ASN][1000 genomes]
rs2839250	0.90[ASN][1000 genomes]
rs2839258	0.91[ASN][1000 genomes]
rs2839269	0.90[ASN][1000 genomes]
rs2839277	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839278	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839279	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839281	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2839287	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2839288	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2839290	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839295	0.88[ASN][1000 genomes]
rs2839302	0.86[ASN][1000 genomes]
rs2839304	0.86[ASN][1000 genomes]
rs2839311	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2839312	0.86[ASN][1000 genomes]
rs2839314	0.86[ASN][1000 genomes]
rs28613801	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28702984	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4276098	0.88[ASN][1000 genomes]
rs4347941	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55744579	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56016846	0.84[ASN][1000 genomes]
rs56134005	0.89[ASN][1000 genomes]
rs56157650	0.86[ASN][1000 genomes]
rs60135034	0.91[ASN][1000 genomes]
rs60407402	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6518299	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6518300	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66799972	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718496	0.92[ASN][1000 genomes]
rs721131	0.86[ASN][1000 genomes]
rs725970	0.83[ASN][1000 genomes]
rs7277986	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7279002	0.92[ASN][1000 genomes]
rs7282515	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73152849	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8127582	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8129305	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8129793	0.81[ASN][1000 genomes]
rs8130209	0.85[ASN][1000 genomes]
rs8132725	0.84[ASN][1000 genomes]
rs9306156	0.84[ASN][1000 genomes]
rs9306157	0.86[ASN][1000 genomes]
rs9637220	0.90[ASN][1000 genomes]
rs9637225	0.86[ASN][1000 genomes]
rs9647244	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9647245	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9975875	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9979126	0.84[ASN][1000 genomes]
rs9980470	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9981212	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9981387	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
2	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
3	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
4	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
5	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
6	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
7	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
9	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
10	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
11	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
12	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
13	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
14	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
15	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
16	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
17	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
18	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
19	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
20	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
21	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
22	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
23	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
24	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers 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	39 gene(s)	inside rSNPs	n/a
25	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9976530	DIP2A	cis	Whole Blood	GTEx
rs9976530	S100B	cis	Whole Blood	GTEx
rs9976530	MCM3AP	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47880000-47916800	Weak transcription	Aorta	Aorta
2	chr21:47880200-47911600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr21:47880200-47916600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr21:47880400-47916600	Weak transcription	Fetal Kidney	kidney
5	chr21:47880400-47916600	Weak transcription	HSMMtube	muscle
6	chr21:47880400-47918000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr21:47880400-47918200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr21:47880400-47931200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr21:47889600-47918200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr21:47889800-47916800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr21:47892800-47920200	Weak transcription	Small Intestine	intestine
12	chr21:47894800-47912800	Weak transcription	GM12878-XiMat	blood
13	chr21:47899000-47918000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr21:47899200-47916800	Weak transcription	Colon Smooth Muscle	Colon
15	chr21:47900800-47917000	Weak transcription	Colonic Mucosa	Colon
16	chr21:47903400-47918400	Weak transcription	Brain Substantia Nigra	brain
17	chr21:47903600-47912200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr21:47903600-47912200	Weak transcription	Brain Angular Gyrus	brain
19	chr21:47903600-47917000	Weak transcription	Brain Hippocampus Middle	brain
20	chr21:47903600-47918200	Weak transcription	Stomach Mucosa	stomach
21	chr21:47903600-47919200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr21:47904200-47911600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:47904200-47911600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr21:47904200-47918600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr21:47904200-47920200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr21:47904200-47920200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr21:47904200-47931200	Weak transcription	Psoas Muscle	Psoas
28	chr21:47904400-47918000	Weak transcription	Pancreas	Pancrea
29	chr21:47904600-47920200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr21:47904800-47918800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr21:47904800-47920200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr21:47905000-47920000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr21:47905000-47920600	Strong transcription	Placenta	Placenta
34	chr21:47905200-47919200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr21:47905400-47919200	Strong transcription	Primary T cells from cord blood	blood
36	chr21:47905400-47919200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr21:47905800-47920200	Strong transcription	Liver	Liver
38	chr21:47906000-47914800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr21:47906200-47914800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr21:47906200-47920400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr21:47906600-47913000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr21:47906600-47913000	Strong transcription	Brain Germinal Matrix	brain
43	chr21:47906800-47918000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr21:47907000-47912200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr21:47907000-47914200	Weak transcription	K562	blood
46	chr21:47907000-47918000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr21:47907200-47911400	Weak transcription	Osteobl	bone
48	chr21:47907200-47913000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr21:47907200-47914600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr21:47907400-47911600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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