Variant report

Variant	rs2254072
Chromosome Location	chr21:45381713-45381714
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF3	chr21:45381045-45381731	GM12878	blood:	n/a	n/a
2	NFIC	chr21:45381015-45381816	GM12878	blood:	n/a	n/a
3	STAT5A	chr21:45381477-45381794	GM12878	blood:	n/a	n/a
4	BCL3	chr21:45381040-45381874	GM12878	blood:	n/a	n/a
5	NFATC1	chr21:45381006-45381814	GM12878	blood:	n/a	n/a
6	MTA3	chr21:45381280-45381865	GM12878	blood:	n/a	n/a
7	BCL3	chr21:45381019-45381770	GM12878	blood:	n/a	n/a
8	PML	chr21:45381032-45381754	GM12878	blood:	n/a	n/a
9	NFIC	chr21:45381029-45381753	GM12878	blood:	n/a	n/a
10	PBX3	chr21:45381060-45381762	GM12878	blood:	n/a	n/a
11	STAT5A	chr21:45380992-45381728	GM12878	blood:	n/a	chr21:45381099-45381111
12	NFATC1	chr21:45381037-45381831	GM12878	blood:	n/a	n/a
13	POLR2A	chr21:45381012-45381771	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45377181..45380868-chr21:45381131..45384623,4	K562	blood:
2	chr21:45375996..45377603-chr21:45380866..45383184,2	MCF-7	breast:
3	chr21:45374823..45379974-chr21:45380727..45386042,6	K562	blood:
4	chr21:45229167..45230861-chr21:45380337..45383260,2	K562	blood:
5	chr21:45373248..45376650-chr21:45380106..45384275,6	K562	blood:

No data

Variant related genes	Relation type
AGPAT3	TF binding region
ENSG00000215458	Chromatin interaction
ENSG00000160216	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs14151	0.95[CHB][hapmap]
rs2000788	0.95[ASN][1000 genomes]
rs2070544	0.90[ASN][1000 genomes]
rs2838447	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838449	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838450	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2838455	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2838458	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3788092	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3788096	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3827251	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4818874	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818875	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4818877	0.96[ASN][1000 genomes]
rs4819353	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4819354	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57524571	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59443212	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61033068	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61639188	0.96[EUR][1000 genomes]
rs7276207	0.82[CHB][hapmap]
rs7282631	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs915876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9974326	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9982600	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9983354	0.90[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv913888	chr21:45351206-45428278	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv913889	chr21:45361044-45414119	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2254072	AGPAT3	cis	Lymphoblastoid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45359400-45389000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr21:45369400-45388800	Weak transcription	Colon Smooth Muscle	Colon
3	chr21:45370000-45384000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr21:45370000-45390200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr21:45373000-45395200	Strong transcription	Fetal Intestine Small	intestine
6	chr21:45374400-45392400	Weak transcription	Stomach Mucosa	stomach
7	chr21:45375200-45395400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr21:45377000-45382400	Weak transcription	HUVEC	blood vessel
9	chr21:45377000-45398400	Weak transcription	A549	lung
10	chr21:45377000-45400800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr21:45377200-45389000	Weak transcription	Psoas Muscle	Psoas
12	chr21:45378000-45390200	Weak transcription	Primary B cells from cord blood	blood
13	chr21:45378200-45383400	Strong transcription	K562	blood
14	chr21:45378200-45395000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr21:45378200-45403800	Strong transcription	Dnd41	blood
16	chr21:45378400-45395000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr21:45378600-45381800	Strong transcription	Fetal Lung	lung
18	chr21:45378600-45381800	Strong transcription	HepG2	liver
19	chr21:45378600-45392800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr21:45378600-45394800	Weak transcription	Fetal Brain Male	brain
21	chr21:45378600-45400800	Weak transcription	NH-A	brain
22	chr21:45378800-45381800	Strong transcription	NHEK	skin
23	chr21:45378800-45382400	Weak transcription	Hela-S3	cervix
24	chr21:45378800-45382800	Strong transcription	Primary T cells from cord blood	blood
25	chr21:45378800-45395000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr21:45378800-45420200	Weak transcription	Right Atrium	heart
27	chr21:45379000-45381800	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr21:45379000-45382000	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr21:45379000-45383400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr21:45379000-45392400	Strong transcription	Fetal Stomach	stomach
31	chr21:45379000-45393400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr21:45379000-45406000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr21:45379200-45381800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr21:45379200-45381800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr21:45379200-45381800	Strong transcription	Fetal Brain Female	brain
36	chr21:45379200-45381800	Strong transcription	Ovary	ovary
37	chr21:45379200-45382600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr21:45379200-45382800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr21:45379200-45383200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr21:45379200-45383200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr21:45379200-45383400	Strong transcription	Liver	Liver
42	chr21:45379200-45384000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr21:45379200-45385200	Weak transcription	Fetal Heart	heart
44	chr21:45379400-45381800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr21:45379400-45381800	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr21:45379400-45381800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr21:45379400-45381800	Strong transcription	Placenta	Placenta
48	chr21:45379400-45381800	Strong transcription	Pancreas	Pancrea
49	chr21:45379400-45382000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr21:45379400-45382000	Strong transcription	Primary T cells fromperipheralblood	blood

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