Variant report

Variant	rs3099976
Chromosome Location	chr2:39049667-39049668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:39049504-39049719	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38976711..38978630-chr2:39046785..39050084,3	K562	blood:
2	chr2:39045661..39047952-chr2:39049221..39051598,2	K562	blood:

Variant related genes	Relation type
DHX57	TF binding region
ENSG00000163214	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs3099986	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3112145	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3112146	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3112148	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39009200-39050000	Weak transcription	HMEC	breast
3	chr2:39009200-39052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
6	chr2:39024000-39053000	Weak transcription	Psoas Muscle	Psoas
7	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
9	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:39033000-39053000	Weak transcription	Fetal Brain Male	brain
11	chr2:39033800-39050200	Weak transcription	K562	blood
12	chr2:39036000-39054000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:39036400-39051600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:39037200-39055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:39037400-39052000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:39037400-39054000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:39037400-39054000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr2:39037400-39054600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:39037800-39053800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:39038200-39056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:39038800-39049800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:39038800-39102200	Weak transcription	Gastric	stomach
24	chr2:39039000-39050000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:39039000-39050000	Weak transcription	NHDF-Ad	bronchial
26	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
28	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
30	chr2:39039200-39049800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:39040000-39069000	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:39040200-39050000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:39040600-39056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:39040800-39049800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:39040800-39054200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:39042800-39063000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
38	chr2:39043200-39051200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:39043200-39052600	Weak transcription	Aorta	Aorta
40	chr2:39043400-39050000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:39043400-39053000	Weak transcription	Brain Substantia Nigra	brain
42	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
43	chr2:39043800-39049800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:39043800-39053000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:39043800-39053800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr2:39044800-39056800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:39045000-39050000	Weak transcription	Dnd41	blood
48	chr2:39045200-39050000	Weak transcription	NHEK	skin
49	chr2:39045800-39052800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:39046000-39049800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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