Variant report

Variant	rs2838452
Chromosome Location	chr21:45382861-45382862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr21:45381778..45384754-chr21:45391171..45392766,2	K562	blood:
4	chr21:45374823..45379974-chr21:45380727..45386042,6	K562	blood:
5	chr21:45229167..45230861-chr21:45380337..45383260,2	K562	blood:
6	chr21:45373248..45376650-chr21:45380106..45384275,6	K562	blood:

Variant related genes	Relation type
ENSG00000160216	Chromatin interaction
ENSG00000215458	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2000787	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003774	1.00[CHB][hapmap]
rs2838448	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2838453	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838454	0.96[ASN][1000 genomes]
rs2838459	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2838463	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs3737358	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[ASN][1000 genomes]
rs57209759	0.88[EUR][1000 genomes]
rs6518340	1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6518342	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276691	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7281203	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283150	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73373134	0.84[ASN][1000 genomes]
rs73906701	0.81[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2838452	AGPAT3	cis	cerebellum	SCAN
rs2838452	PKNOX1	cis	cerebellum	SCAN

Chromatin state (count:113 , 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	chr21:45377000-45398400	Weak transcription	A549	lung
9	chr21:45377000-45400800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr21:45377200-45389000	Weak transcription	Psoas Muscle	Psoas
11	chr21:45378000-45390200	Weak transcription	Primary B cells from cord blood	blood
12	chr21:45378200-45383400	Strong transcription	K562	blood
13	chr21:45378200-45395000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr21:45378200-45403800	Strong transcription	Dnd41	blood
15	chr21:45378400-45395000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr21:45378600-45392800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr21:45378600-45394800	Weak transcription	Fetal Brain Male	brain
18	chr21:45378600-45400800	Weak transcription	NH-A	brain
19	chr21:45378800-45395000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr21:45378800-45420200	Weak transcription	Right Atrium	heart
21	chr21:45379000-45383400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr21:45379000-45392400	Strong transcription	Fetal Stomach	stomach
23	chr21:45379000-45393400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr21:45379000-45406000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr21:45379200-45383200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr21:45379200-45383200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr21:45379200-45383400	Strong transcription	Liver	Liver
28	chr21:45379200-45384000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr21:45379200-45385200	Weak transcription	Fetal Heart	heart
30	chr21:45379400-45383400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr21:45379400-45383400	Strong transcription	Fetal Muscle Leg	muscle
32	chr21:45379400-45384000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr21:45379400-45384800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr21:45379400-45386000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr21:45379400-45386800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr21:45379600-45383000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr21:45379600-45383600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr21:45379600-45405000	Weak transcription	NHDF-Ad	bronchial
39	chr21:45379800-45383200	Strong transcription	Fetal Intestine Large	intestine
40	chr21:45379800-45383400	Strong transcription	Lung	lung
41	chr21:45379800-45383600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr21:45379800-45388600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr21:45380000-45383800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr21:45380200-45383200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr21:45380200-45386600	Weak transcription	Brain Germinal Matrix	brain
46	chr21:45380200-45395000	Weak transcription	HMEC	breast
47	chr21:45380400-45385000	Weak transcription	Thymus	Thymus
48	chr21:45380400-45385800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr21:45380400-45387600	Weak transcription	NHLF	lung
50	chr21:45380400-45391800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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