Variant report

Variant	rs2249970
Chromosome Location	chr21:47864813-47864814
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47863341..47867435-chr21:47876892..47880530,6	MCF-7	breast:
2	chr21:47850253..47852501-chr21:47862918..47865915,2	MCF-7	breast:
3	chr21:47862357..47865195-chr21:47870982..47877612,5	K562	blood:
4	chr21:47860237..47862414-chr21:47862765..47864935,2	K562	blood:
5	chr21:47856896..47861737-chr21:47863435..47865774,4	K562	blood:
6	chr21:47829908..47831983-chr21:47862794..47864924,2	K562	blood:
7	chr21:47858571..47860642-chr21:47862519..47864961,2	MCF-7	breast:
8	chr21:47863005..47865990-chr21:47875934..47878581,2	MCF-7	breast:
9	chr21:47863796..47865408-chr21:47870783..47872310,2	MCF-7	breast:
10	chr21:47850026..47853231-chr21:47864419..47867028,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000160299	Chromatin interaction
ENSG00000160305	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1029262	0.91[ASN][1000 genomes]
rs11089066	0.90[ASN][1000 genomes]
rs11089068	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11089069	0.94[ASN][1000 genomes]
rs11089071	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11089072	0.90[ASN][1000 genomes]
rs1123540	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12185864	0.90[ASN][1000 genomes]
rs12482279	0.92[ASN][1000 genomes]
rs12483081	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12483421	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12626200	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12626961	0.90[ASN][1000 genomes]
rs12627331	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12627653	0.91[ASN][1000 genomes]
rs13047052	0.89[ASN][1000 genomes]
rs1977907	0.89[ASN][1000 genomes]
rs2012217	0.91[ASN][1000 genomes]
rs2032111	0.95[ASN][1000 genomes]
rs2051190	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2070426	0.94[ASN][1000 genomes]
rs2070434	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2073374	0.96[ASN][1000 genomes]
rs2073376	0.95[ASN][1000 genomes]
rs2073377	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2073381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300563	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2330594	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839257	0.95[ASN][1000 genomes]
rs2839261	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839265	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839268	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839270	0.91[ASN][1000 genomes]
rs2839275	0.95[ASN][1000 genomes]
rs2839276	0.95[ASN][1000 genomes]
rs2839280	0.92[ASN][1000 genomes]
rs2839284	0.94[ASN][1000 genomes]
rs2839285	0.94[ASN][1000 genomes]
rs2839296	0.89[ASN][1000 genomes]
rs2839297	0.90[ASN][1000 genomes]
rs2839299	0.82[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	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3747010	0.92[ASN][1000 genomes]
rs4267585	0.90[ASN][1000 genomes]
rs4431027	0.91[ASN][1000 genomes]
rs4819256	0.90[ASN][1000 genomes]
rs59500178	0.89[ASN][1000 genomes]
rs59977673	0.90[ASN][1000 genomes]
rs62224256	0.87[ASN][1000 genomes]
rs62224257	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62224258	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62225682	0.87[ASN][1000 genomes]
rs7279991	0.94[ASN][1000 genomes]
rs8132022	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9789884	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9975345	0.92[ASN][1000 genomes]
rs9984247	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 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	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv914138	chr21:47700498-47866227	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
19	nsv914140	chr21:47712185-47866227	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a
20	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
21	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
22	nsv914142	chr21:47772468-47866227	Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
23	nsv914144	chr21:47792874-47866227	Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
24	nsv587995	chr21:47803949-47877594	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
25	nsv914145	chr21:47804438-47866227	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
26	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
27	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
28	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
29	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
30	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2249970	MCM3AP	Cis_1M	lymphoblastoid	RTeQTL
rs2249970	DIP2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47803200-47872400	Weak transcription	Fetal Kidney	kidney
2	chr21:47827400-47866600	Strong transcription	Fetal Stomach	stomach
3	chr21:47828600-47872400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr21:47829400-47867800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr21:47834000-47868200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr21:47834200-47868200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr21:47836800-47872400	Weak transcription	Right Atrium	heart
8	chr21:47843400-47867400	Strong transcription	Dnd41	blood
9	chr21:47843800-47867600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr21:47843800-47868400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr21:47844200-47866800	Strong transcription	Brain Germinal Matrix	brain
12	chr21:47844200-47867400	Strong transcription	Fetal Brain Female	brain
13	chr21:47844800-47865800	Strong transcription	Duodenum Mucosa	Duodenum
14	chr21:47844800-47867400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr21:47845200-47867400	Strong transcription	Thymus	Thymus
16	chr21:47845400-47867400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr21:47845600-47867200	Strong transcription	Fetal Muscle Leg	muscle
18	chr21:47845600-47877400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr21:47846400-47865600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr21:47847000-47865600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr21:47847000-47865600	Strong transcription	Liver	Liver
22	chr21:47847600-47866800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr21:47851000-47876000	Weak transcription	Small Intestine	intestine
24	chr21:47852200-47867800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr21:47853200-47866800	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr21:47854000-47865000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr21:47854000-47866000	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr21:47854000-47868000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr21:47854400-47866400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr21:47854600-47865800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr21:47854600-47866600	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr21:47854600-47866800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr21:47855600-47865000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr21:47855600-47865800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr21:47855800-47865000	Strong transcription	HMEC	breast
36	chr21:47856400-47865800	Strong transcription	Hela-S3	cervix
37	chr21:47856800-47865800	Strong transcription	Fetal Intestine Large	intestine
38	chr21:47857400-47865600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr21:47857400-47867400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr21:47857400-47868600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr21:47857600-47867200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr21:47857800-47866000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr21:47857800-47868000	Strong transcription	Placenta	Placenta
44	chr21:47858000-47867800	Strong transcription	Fetal Thymus	thymus
45	chr21:47858200-47866800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr21:47858400-47865600	Strong transcription	Primary T cells from cord blood	blood
47	chr21:47858400-47877400	Weak transcription	Stomach Mucosa	stomach
48	chr21:47860600-47865600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr21:47861200-47874000	Weak transcription	NH-A	brain
50	chr21:47861400-47869600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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