Variant report

Variant	rs57884089
Chromosome Location	chr2:39083649-39083650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38976661..38978798-chr2:39083252..39086476,5	MCF-7	breast:
2	chr2:39075448..39080892-chr2:39081993..39084972,5	K562	blood:
3	chr2:39082200..39083996-chr2:39090256..39092735,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1901290	0.92[ASN][1000 genomes]
rs3099947	0.85[ASN][1000 genomes]
rs3099953	0.92[ASN][1000 genomes]
rs3099997	0.92[ASN][1000 genomes]
rs3112164	0.92[ASN][1000 genomes]
rs3112174	0.92[ASN][1000 genomes]
rs3112176	0.92[ASN][1000 genomes]
rs3112177	0.92[ASN][1000 genomes]
rs56322480	0.92[ASN][1000 genomes]
rs58412684	0.92[ASN][1000 genomes]
rs58645810	0.92[ASN][1000 genomes]
rs59788371	0.92[ASN][1000 genomes]
rs60406386	0.92[ASN][1000 genomes]
rs61393528	0.92[ASN][1000 genomes]
rs6544182	0.85[ASN][1000 genomes]
rs6722176	0.92[ASN][1000 genomes]
rs6722478	0.92[ASN][1000 genomes]
rs6748000	0.92[ASN][1000 genomes]
rs73930373	0.92[ASN][1000 genomes]
rs73930374	0.92[ASN][1000 genomes]
rs73930378	0.92[ASN][1000 genomes]
rs7571935	0.92[ASN][1000 genomes]
rs7605183	0.92[ASN][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	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 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	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
3	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:39038800-39102200	Weak transcription	Gastric	stomach
5	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
7	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
9	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:39055200-39085600	Weak transcription	Psoas Muscle	Psoas
11	chr2:39057000-39086200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:39058000-39087800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:39063600-39088400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:39067200-39090200	Weak transcription	Stomach Mucosa	stomach
15	chr2:39068400-39090600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:39072200-39095400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:39072400-39089200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:39072600-39090800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:39073000-39091200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:39073600-39090200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:39075200-39090800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:39076000-39090600	Strong transcription	Brain Germinal Matrix	brain
23	chr2:39076200-39090600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:39076400-39090800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:39076600-39090800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:39078000-39090800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:39078200-39091200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:39078400-39090600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:39078800-39084000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:39078800-39090600	Strong transcription	Osteobl	bone
31	chr2:39079200-39086000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:39079200-39086200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:39079400-39090800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr2:39079600-39086200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:39079600-39090400	Strong transcription	Fetal Thymus	thymus
36	chr2:39079600-39090800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:39079600-39090800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:39079600-39090800	Strong transcription	Fetal Brain Female	brain
39	chr2:39079800-39084000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:39079800-39084000	Strong transcription	Brain Angular Gyrus	brain
41	chr2:39079800-39084200	Strong transcription	Ovary	ovary
42	chr2:39079800-39084600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr2:39079800-39085800	Strong transcription	Thymus	Thymus
44	chr2:39079800-39086600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:39079800-39086600	Strong transcription	Liver	Liver
46	chr2:39079800-39089600	Strong transcription	Fetal Stomach	stomach
47	chr2:39079800-39090600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:39079800-39090600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:39079800-39090600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:39079800-39090600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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