Variant report

Variant	rs62224257
Chromosome Location	chr21:47888265-47888266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47887604..47890529-chr21:47890644..47893911,5	K562	blood:
2	chr21:47878933..47880849-chr21:47887443..47889198,2	MCF-7	breast:
3	chr21:47874840..47880520-chr21:47886599..47894853,12	K562	blood:
4	chr21:47881557..47884744-chr21:47886955..47890913,5	K562	blood:

Variant related genes	Relation type
ENSG00000160305	Chromatin interaction
ENSG00000223692	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1029262	0.91[ASN][1000 genomes]
rs11089066	0.93[ASN][1000 genomes]
rs11089068	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089069	0.97[ASN][1000 genomes]
rs11089071	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11089072	0.90[ASN][1000 genomes]
rs1123540	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12185864	0.93[ASN][1000 genomes]
rs12482279	0.95[ASN][1000 genomes]
rs12483081	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12483421	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12626200	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12626961	0.90[ASN][1000 genomes]
rs12627331	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12627653	0.91[ASN][1000 genomes]
rs13047052	0.89[ASN][1000 genomes]
rs1977907	0.89[ASN][1000 genomes]
rs2012217	0.88[ASN][1000 genomes]
rs2032111	0.98[ASN][1000 genomes]
rs2051190	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070426	0.91[ASN][1000 genomes]
rs2070434	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2073374	0.93[ASN][1000 genomes]
rs2073376	0.92[ASN][1000 genomes]
rs2073377	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2073381	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249970	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300563	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2330594	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839257	0.92[ASN][1000 genomes]
rs2839261	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839265	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839268	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839270	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2839275	0.98[ASN][1000 genomes]
rs2839276	0.98[ASN][1000 genomes]
rs2839280	0.95[ASN][1000 genomes]
rs2839284	0.97[ASN][1000 genomes]
rs2839285	0.97[ASN][1000 genomes]
rs2839296	0.89[ASN][1000 genomes]
rs2839297	0.90[ASN][1000 genomes]
rs2839299	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2839313	0.92[ASN][1000 genomes]
rs2839317	0.90[ASN][1000 genomes]
rs34590323	0.89[ASN][1000 genomes]
rs34736293	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747010	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4267585	0.90[ASN][1000 genomes]
rs4431027	0.91[ASN][1000 genomes]
rs4819256	0.93[ASN][1000 genomes]
rs59500178	0.86[ASN][1000 genomes]
rs59977673	0.90[ASN][1000 genomes]
rs62224256	0.90[ASN][1000 genomes]
rs62224258	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62225682	0.87[ASN][1000 genomes]
rs7279991	0.97[ASN][1000 genomes]
rs8132022	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9789884	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9975345	0.89[ASN][1000 genomes]
rs9984247	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
2	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv914136	chr21:47681041-47900994	Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	n/a
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	esv2762115	chr21:47885139-47895430	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62224257	DIP2A	Cis_1M	lymphoblastoid	RTeQTL
rs62224257	MCM3AP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47879800-47892000	Weak transcription	Lung	lung
2	chr21:47880000-47889400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:47880000-47892000	Weak transcription	Liver	Liver
4	chr21:47880000-47892000	Weak transcription	Small Intestine	intestine
5	chr21:47880000-47892200	Weak transcription	Pancreas	Pancrea
6	chr21:47880000-47892200	Weak transcription	Spleen	Spleen
7	chr21:47880000-47892400	Weak transcription	Gastric	stomach
8	chr21:47880000-47900200	Weak transcription	Esophagus	oesophagus
9	chr21:47880000-47900400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:47880000-47905800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr21:47880000-47916800	Weak transcription	Aorta	Aorta
12	chr21:47880200-47889000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr21:47880200-47889400	Weak transcription	Fetal Intestine Small	intestine
14	chr21:47880200-47892400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr21:47880200-47900000	Weak transcription	Colonic Mucosa	Colon
16	chr21:47880200-47902800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr21:47880200-47903200	Weak transcription	Stomach Mucosa	stomach
18	chr21:47880200-47909400	Weak transcription	A549	lung
19	chr21:47880200-47911600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr21:47880200-47916600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr21:47880400-47888800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr21:47880400-47889000	Weak transcription	Primary B cells from cord blood	blood
23	chr21:47880400-47889000	Weak transcription	Osteobl	bone
24	chr21:47880400-47889200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr21:47880400-47889200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr21:47880400-47889200	Weak transcription	Thymus	Thymus
27	chr21:47880400-47890400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr21:47880400-47891400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr21:47880400-47892000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr21:47880400-47892200	Weak transcription	Right Ventricle	heart
31	chr21:47880400-47893800	Weak transcription	Fetal Intestine Large	intestine
32	chr21:47880400-47896800	Weak transcription	Fetal Lung	lung
33	chr21:47880400-47898800	Weak transcription	HSMM	muscle
34	chr21:47880400-47906600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr21:47880400-47908800	Weak transcription	Fetal Brain Male	brain
36	chr21:47880400-47908800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr21:47880400-47909200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr21:47880400-47909200	Weak transcription	NHLF	lung
39	chr21:47880400-47909400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr21:47880400-47916600	Weak transcription	Fetal Kidney	kidney
41	chr21:47880400-47916600	Weak transcription	HSMMtube	muscle
42	chr21:47880400-47918000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr21:47880400-47918200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr21:47880400-47931200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr21:47880600-47889200	Weak transcription	NH-A	brain
46	chr21:47880600-47890800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr21:47880600-47892000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr21:47880800-47902600	Weak transcription	Brain Angular Gyrus	brain
49	chr21:47881000-47889200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr21:47881200-47889000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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