Variant report

Variant	rs3856688
Chromosome Location	chr3:139396462-139396463
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139395742..139397404-chr3:139400797..139402363,2	K562	blood:

Variant related genes	Relation type
ENSG00000261763	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10804669	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10935343	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714276	0.88[ASN][1000 genomes]
rs11717254	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11720063	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720212	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720232	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12492528	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12639448	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28451114	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3922621	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3922941	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4234472	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4683678	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683680	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55983509	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59525705	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7633367	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9784259	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3431059	chr3:139395962-139398210	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139395200-139396800	Enhancers	Fetal Brain Male	brain
2	chr3:139395600-139397200	Active TSS	Primary T cells from cord blood	blood
3	chr3:139395600-139397200	Active TSS	Fetal Kidney	kidney
4	chr3:139395600-139397200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:139395800-139396600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:139395800-139396600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
7	chr3:139395800-139396600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:139395800-139396800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:139395800-139396800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr3:139395800-139397200	Active TSS	Ovary	ovary
11	chr3:139395800-139397400	Active TSS	Brain Cingulate Gyrus	brain
12	chr3:139395800-139397400	Active TSS	Right Atrium	heart
13	chr3:139395800-139397800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:139396000-139396600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:139396000-139396600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr3:139396000-139396600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:139396000-139396600	Flanking Active TSS	Liver	Liver
18	chr3:139396000-139396600	Flanking Active TSS	Colonic Mucosa	Colon
19	chr3:139396000-139396600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
20	chr3:139396000-139396600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
21	chr3:139396000-139396600	Flanking Active TSS	Fetal Thymus	thymus
22	chr3:139396000-139396800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr3:139396000-139396800	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr3:139396000-139396800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:139396000-139396800	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr3:139396000-139396800	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
27	chr3:139396000-139396800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:139396000-139396800	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr3:139396000-139396800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
30	chr3:139396000-139396800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
31	chr3:139396000-139396800	Active TSS	A549	lung
32	chr3:139396000-139396800	Active TSS	Hela-S3	cervix
33	chr3:139396000-139397200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:139396000-139397400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr3:139396000-139397400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr3:139396000-139397400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
37	chr3:139396000-139397400	Active TSS	Fetal Brain Female	brain
38	chr3:139396200-139396600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:139396200-139396600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr3:139396200-139396600	Flanking Active TSS	Lung	lung
41	chr3:139396200-139396600	Flanking Active TSS	Spleen	Spleen
42	chr3:139396200-139396600	Flanking Active TSS	GM12878-XiMat	blood
43	chr3:139396200-139396600	Active TSS	NH-A	brain
44	chr3:139396200-139396800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:139396200-139396800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:139396200-139396800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:139396200-139396800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:139396200-139396800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:139396200-139396800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:139396200-139396800	Flanking Active TSS	Primary B cells from cord blood	blood

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