Variant report

Variant	rs59540955
Chromosome Location	chr3:138656537-138656538
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:138655209..138657640-chr3:138920861..138922707,2	MCF-7	breast:
2	chr3:138655774..138657700-chr3:138692387..138694349,2	K562	blood:
3	chr3:138655102..138656710-chr3:138945646..138947395,2	K562	blood:
4	chr3:138654402..138658110-chr3:139047575..139051045,3	K562	blood:
5	chr3:138655696..138657918-chr3:138697620..138699294,2	K562	blood:
6	chr3:138369214..138371379-chr3:138655274..138656934,2	K562	blood:
7	chr3:138654619..138656713-chr3:138694256..138696204,2	K562	blood:

No data

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12630172	1.00[EUR][1000 genomes]
rs1482976	1.00[EUR][1000 genomes]
rs2291252	1.00[EUR][1000 genomes]
rs57383887	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72976914	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72976918	1.00[EUR][1000 genomes]
rs750321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv877540	chr3:138645013-138670695	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv877541	chr3:138645013-138673922	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv877542	chr3:138645013-138750904	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138654400-138656600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:138654600-138656600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:138654600-138657400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
4	chr3:138654600-138657600	Enhancers	Pancreas	Pancrea
5	chr3:138654600-138657800	Bivalent Enhancer	Stomach Mucosa	stomach
6	chr3:138654600-138659200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:138654800-138659000	Bivalent Enhancer	Liver	Liver
8	chr3:138655200-138657600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:138655200-138659000	Bivalent Enhancer	Placenta	Placenta
10	chr3:138655200-138659000	Bivalent Enhancer	Fetal Thymus	thymus
11	chr3:138655200-138659200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:138655200-138659200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr3:138655400-138656600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:138655400-138656800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
15	chr3:138655400-138656800	Bivalent Enhancer	Esophagus	oesophagus
16	chr3:138655400-138658200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:138655400-138658200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr3:138655400-138658600	Bivalent Enhancer	Fetal Stomach	stomach
19	chr3:138655400-138659000	Bivalent Enhancer	Left Ventricle	heart
20	chr3:138655400-138659200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
21	chr3:138655400-138659200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
22	chr3:138655400-138659200	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr3:138655600-138656600	Bivalent Enhancer	Fetal Intestine Large	intestine
24	chr3:138655600-138656800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:138655600-138656800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:138655600-138656800	Bivalent Enhancer	Brain Germinal Matrix	brain
27	chr3:138655600-138657200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr3:138655600-138657600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:138655600-138657600	Bivalent Enhancer	Lung	lung
30	chr3:138655600-138657800	Bivalent Enhancer	Fetal Heart	heart
31	chr3:138655600-138658800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
32	chr3:138655600-138659000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr3:138655600-138659000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
34	chr3:138655600-138659200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:138655600-138659200	Bivalent Enhancer	Fetal Intestine Small	intestine
36	chr3:138655600-138659200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr3:138655800-138656600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
38	chr3:138655800-138656600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:138655800-138656600	Bivalent Enhancer	Brain Angular Gyrus	brain
40	chr3:138655800-138656600	Weak transcription	Right Atrium	heart
41	chr3:138655800-138656800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
42	chr3:138655800-138657000	Bivalent Enhancer	Primary T cells from cord blood	blood
43	chr3:138655800-138657200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
44	chr3:138655800-138657200	Bivalent Enhancer	NH-A	brain
45	chr3:138655800-138657200	Bivalent Enhancer	NHEK	skin
46	chr3:138655800-138657400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
47	chr3:138655800-138657600	Flanking Active TSS	Ovary	ovary
48	chr3:138655800-138657800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
49	chr3:138655800-138658200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
50	chr3:138655800-138658200	Bivalent Enhancer	HMEC	breast

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