Variant report

Variant	rs12539339
Chromosome Location	chr7:140097554-140097555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140097102..140100754-chr7:140100879..140105218,4	MCF-7	breast:
2	chr7:140096834..140099391-chr7:140178947..140180902,2	K562	blood:
3	chr7:140091825..140093719-chr7:140095231..140098227,2	MCF-7	breast:
4	chr7:139875282..139878278-chr7:140096376..140098840,2	MCF-7	breast:
5	chr7:140075069..140077735-chr7:140096588..140099526,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146955	Chromatin interaction
ENSG00000157800	Chromatin interaction
ENSG00000133606	Chromatin interaction
ENSG00000238868	Chromatin interaction
ENSG00000260231	Chromatin interaction
ENSG00000006459	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs67892123	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12539339	DENND2A	cis	brain	BrainEAC

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140080200-140097600	Weak transcription	Brain Angular Gyrus	brain
2	chr7:140090800-140097600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:140090800-140097600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:140090800-140097600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:140090800-140097600	Weak transcription	Spleen	Spleen
6	chr7:140092200-140097600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:140093400-140097600	Weak transcription	Lung	lung
8	chr7:140093800-140097600	Weak transcription	Left Ventricle	heart
9	chr7:140095800-140097600	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr7:140095800-140097800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:140096000-140097600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
12	chr7:140096000-140097600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:140096000-140097600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr7:140096000-140097600	Enhancers	Stomach Mucosa	stomach
15	chr7:140096000-140098800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:140096200-140098400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:140096400-140097600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:140096400-140097800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr7:140096400-140098600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:140096600-140097600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:140096600-140097600	Weak transcription	Brain Substantia Nigra	brain
22	chr7:140096600-140097600	Enhancers	Fetal Muscle Trunk	muscle
23	chr7:140096600-140098600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr7:140096600-140098600	Active TSS	K562	blood
25	chr7:140096800-140097600	Weak transcription	Small Intestine	intestine
26	chr7:140096800-140098600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:140096800-140098600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:140096800-140098800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:140097000-140097600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr7:140097000-140097800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:140097000-140098400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:140097000-140098600	Active TSS	Colonic Mucosa	Colon
33	chr7:140097000-140098600	Active TSS	Fetal Brain Female	brain
34	chr7:140097200-140097600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr7:140097200-140097600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:140097200-140097600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr7:140097200-140097600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:140097200-140097600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:140097200-140097600	Flanking Active TSS	HUVEC	blood vessel
40	chr7:140097200-140097800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr7:140097200-140097800	Flanking Active TSS	Hela-S3	cervix
42	chr7:140097200-140097800	Flanking Active TSS	Osteobl	bone
43	chr7:140097200-140098000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:140097200-140098000	Active TSS	Brain Germinal Matrix	brain
45	chr7:140097200-140098000	Flanking Active TSS	Dnd41	blood
46	chr7:140097200-140098400	Active TSS	H9 Cell Line	embryonic stem cell
47	chr7:140097200-140098400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:140097200-140098400	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr7:140097200-140098400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:140097200-140098400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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