Variant report

Variant	rs2838450
Chromosome Location	chr21:45380130-45380131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45371946..45375677-chr21:45376772..45380405,4	K562	blood:
2	chr21:45378072..45381016-chr21:45430291..45432652,2	K562	blood:
3	chr21:45373248..45376650-chr21:45380106..45384275,6	K562	blood:

Variant related genes	Relation type
ENSG00000160218	Chromatin interaction
ENSG00000160216	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1058694	1.00[CHB][hapmap]
rs12626709	0.85[ASN][1000 genomes]
rs2254072	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2838447	1.00[CEU][hapmap]
rs2838449	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2838456	0.95[CHB][hapmap]
rs2838460	0.95[CHB][hapmap]
rs3788092	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3788094	0.95[CHB][hapmap]
rs3788095	0.89[CHB][hapmap]
rs3827249	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs3827250	0.81[ASN][1000 genomes]
rs3827251	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818874	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4818875	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4819353	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819354	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4819356	0.89[CHB][hapmap]
rs57524571	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59443212	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61033068	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61639188	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7281359	0.80[ASN][1000 genomes]
rs7435	1.00[CHB][hapmap]
rs915876	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9647232	0.87[ASN][1000 genomes]
rs9974326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9978441	0.89[CHB][hapmap]
rs9982600	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	esv3397810	chr21:45376824-45380622	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3341187	chr21:45378374-45380872	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838450	AGPAT3	cis	Lymphoblastoid	GTEx

Chromatin state (count:114 , 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	chr21:45369600-45381200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr21:45370000-45381200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr21:45370000-45384000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr21:45370000-45390200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr21:45373000-45395200	Strong transcription	Fetal Intestine Small	intestine
8	chr21:45373800-45381000	Weak transcription	HSMM	muscle
9	chr21:45374200-45380200	Weak transcription	HSMMtube	muscle
10	chr21:45374400-45392400	Weak transcription	Stomach Mucosa	stomach
11	chr21:45375200-45395400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr21:45376600-45380200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr21:45377000-45382400	Weak transcription	HUVEC	blood vessel
14	chr21:45377000-45398400	Weak transcription	A549	lung
15	chr21:45377000-45400800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr21:45377200-45389000	Weak transcription	Psoas Muscle	Psoas
17	chr21:45378000-45390200	Weak transcription	Primary B cells from cord blood	blood
18	chr21:45378200-45383400	Strong transcription	K562	blood
19	chr21:45378200-45395000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr21:45378200-45403800	Strong transcription	Dnd41	blood
21	chr21:45378400-45380200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr21:45378400-45395000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr21:45378600-45381800	Strong transcription	Fetal Lung	lung
24	chr21:45378600-45381800	Strong transcription	HepG2	liver
25	chr21:45378600-45392800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr21:45378600-45394800	Weak transcription	Fetal Brain Male	brain
27	chr21:45378600-45400800	Weak transcription	NH-A	brain
28	chr21:45378800-45380400	Strong transcription	NHLF	lung
29	chr21:45378800-45381800	Strong transcription	NHEK	skin
30	chr21:45378800-45382400	Weak transcription	Hela-S3	cervix
31	chr21:45378800-45382800	Strong transcription	Primary T cells from cord blood	blood
32	chr21:45378800-45395000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr21:45378800-45420200	Weak transcription	Right Atrium	heart
34	chr21:45379000-45380600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr21:45379000-45381600	Strong transcription	Brain Angular Gyrus	brain
36	chr21:45379000-45381800	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr21:45379000-45382000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr21:45379000-45383400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr21:45379000-45392400	Strong transcription	Fetal Stomach	stomach
40	chr21:45379000-45393400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr21:45379000-45406000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr21:45379200-45380200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
43	chr21:45379200-45380200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr21:45379200-45380400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr21:45379200-45381200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr21:45379200-45381800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr21:45379200-45381800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr21:45379200-45381800	Strong transcription	Fetal Brain Female	brain
49	chr21:45379200-45381800	Strong transcription	Ovary	ovary
50	chr21:45379200-45382600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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