Variant report

Variant	rs9978441
Chromosome Location	chr21:45400234-45400235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45399246..45402021-chr21:45429324..45431485,3	MCF-7	breast:
2	chr21:45390949..45392621-chr21:45399600..45401167,2	K562	blood:
3	chr21:45394072..45397426-chr21:45398939..45402016,4	K562	blood:
4	chr21:45395550..45398275-chr21:45399563..45401306,2	K562	blood:
5	chr21:45390949..45395215-chr21:45399667..45403680,4	K562	blood:
6	chr21:45397719..45400643-chr21:45719972..45722043,2	MCF-7	breast:
7	chr21:45400066..45403685-chr21:45432405..45434021,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141959	Chromatin interaction
ENSG00000160216	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1058694	0.94[CHB][hapmap]
rs11702855	0.80[AMR][1000 genomes]
rs12626709	0.83[ASN][1000 genomes]
rs2070543	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2838450	0.89[CHB][hapmap]
rs2838456	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2838460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788094	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs3788095	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3827249	0.88[CHB][hapmap]
rs3827250	0.82[ASN][1000 genomes]
rs4818876	0.82[ASN][1000 genomes]
rs4819356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819359	0.80[AMR][1000 genomes]
rs62229688	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62229730	0.81[AMR][1000 genomes]
rs7276207	0.89[CEU][hapmap]
rs73226967	0.83[EUR][1000 genomes]
rs7435	0.94[CHB][hapmap]
rs9647232	0.81[ASN][1000 genomes]
rs9974326	0.94[CHB][hapmap]
rs9982600	0.82[CHB][hapmap]
rs9983354	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
rs9978441	AGPAT3	cis	Lymphoblastoid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45377000-45400800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr21:45378200-45403800	Strong transcription	Dnd41	blood
3	chr21:45378600-45400800	Weak transcription	NH-A	brain
4	chr21:45378800-45420200	Weak transcription	Right Atrium	heart
5	chr21:45379000-45406000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr21:45379600-45405000	Weak transcription	NHDF-Ad	bronchial
7	chr21:45381600-45400800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr21:45382000-45402600	Weak transcription	Small Intestine	intestine
9	chr21:45383200-45405400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr21:45383200-45405400	Weak transcription	Hela-S3	cervix
11	chr21:45383400-45405200	Weak transcription	HUVEC	blood vessel
12	chr21:45387600-45401400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr21:45389600-45401200	Weak transcription	Psoas Muscle	Psoas
14	chr21:45391600-45406800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr21:45392000-45406800	Weak transcription	NHEK	skin
16	chr21:45393000-45405200	Weak transcription	HepG2	liver
17	chr21:45393200-45401000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr21:45393200-45413800	Weak transcription	HSMMtube	muscle
19	chr21:45393600-45401000	Weak transcription	Aorta	Aorta
20	chr21:45393800-45400400	Weak transcription	NHLF	lung
21	chr21:45395400-45400600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:45395400-45401000	Weak transcription	Brain Angular Gyrus	brain
23	chr21:45395400-45401400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr21:45395400-45401800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr21:45395400-45403800	Weak transcription	Fetal Kidney	kidney
26	chr21:45395400-45406000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr21:45395600-45400800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr21:45395600-45402000	Weak transcription	Fetal Brain Male	brain
29	chr21:45395600-45404200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr21:45395800-45401000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr21:45395800-45401000	Weak transcription	Brain Substantia Nigra	brain
32	chr21:45395800-45401400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr21:45395800-45405000	Strong transcription	Fetal Intestine Small	intestine
34	chr21:45395800-45405400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr21:45395800-45405600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr21:45396200-45404200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr21:45396600-45403000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr21:45396600-45403600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr21:45396600-45403800	Strong transcription	Liver	Liver
40	chr21:45396600-45404200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr21:45396600-45404200	Strong transcription	Esophagus	oesophagus
42	chr21:45396600-45404200	Strong transcription	Thymus	Thymus
43	chr21:45396600-45404400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr21:45396600-45404800	Strong transcription	Fetal Stomach	stomach
45	chr21:45396800-45403600	Strong transcription	Fetal Intestine Large	intestine
46	chr21:45396800-45405000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr21:45397000-45404200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr21:45397200-45400400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr21:45397200-45402600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr21:45397200-45402800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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