Variant report

Variant	rs10084623
Chromosome Location	chr21:45283670-45283671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr21:45283353-45283697	K562	blood:	n/a	chr21:45283643-45283657 chr21:45283641-45283652 chr21:45283642-45283655
2	MXI1	chr21:45283199-45286803	SK-N-SH	brain:	n/a	n/a
3	SPI1	chr21:45283427-45283702	GM12878	blood:	n/a	n/a
4	POLR2A	chr21:45283396-45283878	GM12878	blood:	n/a	n/a
5	SPI1	chr21:45283418-45283819	GM12891	blood:	n/a	n/a
6	SPI1	chr21:45283418-45283779	GM12891	blood:	n/a	n/a
7	POLR2A	chr21:45283193-45284473	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45282912..45284880-chr21:45350407..45353939,3	K562	blood:
2	chr21:45283298..45287513-chr21:45338855..45343382,5	K562	blood:
3	chr21:45283616..45286882-chr21:45299913..45305661,6	MCF-7	breast:
4	chr21:45281617..45284138-chr21:45284201..45287466,4	MCF-7	breast:
5	chr21:45282036..45289054-chr21:45334704..45338842,9	K562	blood:
6	chr21:45282600..45286741-chr21:45429139..45433009,5	MCF-7	breast:
7	chr21:45226284..45237567-chr21:45281864..45289573,19	K562	blood:
8	chr21:45228592..45232844-chr21:45283509..45286625,5	MCF-7	breast:
9	chr21:45283663..45287678-chr21:45338795..45345768,12	K562	blood:
10	chr21:45240125..45242679-chr21:45283332..45285060,2	MCF-7	breast:
11	chr21:45282912..45284880-chr21:45350407..45352499,2	K562	blood:
12	chr21:45282965..45285916-chr21:45430237..45433854,8	MCF-7	breast:

No data

Variant related genes	Relation type
AGPAT3	TF binding region
ENSG00000160216	Chromatin interaction
ENSG00000215458	Chromatin interaction
ENSG00000160218	Chromatin interaction
ENSG00000199598	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10084560	1.00[AMR][1000 genomes]
rs11909584	1.00[AMR][1000 genomes]
rs60998087	1.00[AMR][1000 genomes]
rs9306170	1.00[AMR][1000 genomes]
rs9974773	1.00[AMR][1000 genomes]
rs9977077	1.00[AMR][1000 genomes]
rs9977718	1.00[AMR][1000 genomes]
rs9981524	1.00[AMR][1000 genomes]
rs9981945	1.00[AMR][1000 genomes]
rs9982231	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs9983454	1.00[AMR][1000 genomes]
rs9985020	0.86[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
3	nsv834107	chr21:45155325-45294546	Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	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
5	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1066284	chr21:45249549-45343314	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv3538	chr21:45267674-45297159	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3389400	chr21:45283349-45286397	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10084623	SIX3	trans	lymphoblastoid	seeQTL
rs10084623	PDGFD	trans	lymphoblastoid	seeQTL
rs10084623	RAB31	trans	lymphoblastoid	seeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45275000-45284000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:45279400-45284000	Weak transcription	Right Ventricle	heart
3	chr21:45280400-45284000	Weak transcription	Colon Smooth Muscle	Colon
4	chr21:45280600-45283800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr21:45280600-45284000	Weak transcription	Fetal Lung	lung
6	chr21:45280800-45283800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:45280800-45283800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr21:45280800-45284000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr21:45280800-45284000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr21:45280800-45284000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr21:45280800-45284000	Weak transcription	Small Intestine	intestine
12	chr21:45280800-45284000	Weak transcription	A549	lung
13	chr21:45280800-45284000	Weak transcription	NHEK	skin
14	chr21:45280800-45284000	Weak transcription	NHLF	lung
15	chr21:45280800-45284200	Weak transcription	Brain Substantia Nigra	brain
16	chr21:45281000-45283800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr21:45281000-45283800	Weak transcription	HMEC	breast
18	chr21:45281000-45284000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr21:45281000-45284000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr21:45281000-45284000	Weak transcription	Spleen	Spleen
21	chr21:45281000-45284200	Weak transcription	Gastric	stomach
22	chr21:45281200-45284000	Weak transcription	Ovary	ovary
23	chr21:45281200-45284000	Weak transcription	Psoas Muscle	Psoas
24	chr21:45281600-45284000	Weak transcription	Left Ventricle	heart
25	chr21:45281600-45284200	Weak transcription	Lung	lung
26	chr21:45281800-45283800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr21:45281800-45284000	Weak transcription	Adipose Nuclei	Adipose
28	chr21:45281800-45284000	Weak transcription	Colonic Mucosa	Colon
29	chr21:45281800-45284000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr21:45282000-45283800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr21:45282000-45284000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr21:45282000-45284000	Weak transcription	Stomach Mucosa	stomach
33	chr21:45282000-45284200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr21:45282000-45284200	Weak transcription	Pancreas	Pancrea
35	chr21:45282200-45283800	Weak transcription	Thymus	Thymus
36	chr21:45283400-45283800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr21:45283400-45284000	Enhancers	Primary B cells from cord blood	blood
38	chr21:45283400-45284000	Enhancers	Primary B cells from peripheral blood	blood
39	chr21:45283400-45284000	Enhancers	Primary hematopoietic stem cells	blood
40	chr21:45283400-45284000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr21:45283400-45284000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr21:45283400-45284000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr21:45283400-45284000	Enhancers	Brain Anterior Caudate	brain
44	chr21:45283400-45284000	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr21:45283400-45284000	Enhancers	K562	blood
46	chr21:45283400-45284200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr21:45283400-45284200	Flanking Active TSS	GM12878-XiMat	blood
48	chr21:45283400-45284400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr21:45283400-45285600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr21:45283600-45283800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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