Variant report

Variant	rs59647542
Chromosome Location	chr3:45858710-45858711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1029732	0.85[ASN][1000 genomes]
rs11916880	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57667195	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61587933	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62245073	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62245074	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62245076	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73830464	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7614952	0.85[ASN][1000 genomes]
rs952287	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45838400-45860000	Weak transcription	Gastric	stomach
2	chr3:45842400-45859200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:45842400-45859800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:45845400-45858800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:45847800-45871400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:45848000-45864400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:45848600-45860800	Weak transcription	Primary T cells from cord blood	blood
8	chr3:45849400-45859000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:45849400-45864800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:45849400-45875200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:45849600-45862400	Weak transcription	Fetal Lung	lung
12	chr3:45849800-45871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:45850000-45859000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:45850000-45859000	Weak transcription	Brain Substantia Nigra	brain
15	chr3:45850000-45859800	Weak transcription	Small Intestine	intestine
16	chr3:45850200-45862200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:45850200-45866200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:45850200-45867800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:45850600-45859000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:45850600-45868200	Weak transcription	Spleen	Spleen
21	chr3:45851000-45861200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:45851600-45859200	Weak transcription	Primary B cells from cord blood	blood
23	chr3:45856000-45859000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:45856000-45862600	Weak transcription	Adipose Nuclei	Adipose
25	chr3:45856200-45859000	Weak transcription	NHLF	lung
26	chr3:45857400-45858800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:45857400-45858800	Enhancers	Psoas Muscle	Psoas
28	chr3:45857400-45859600	Strong transcription	Thymus	Thymus
29	chr3:45857400-45859800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:45857400-45860600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:45857400-45860600	Enhancers	Stomach Smooth Muscle	stomach
32	chr3:45857400-45861200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:45857400-45861600	Enhancers	HMEC	breast
34	chr3:45857400-45861800	Enhancers	HSMMtube	muscle
35	chr3:45857600-45859000	Enhancers	Stomach Mucosa	stomach
36	chr3:45857600-45861400	Enhancers	Fetal Heart	heart
37	chr3:45857600-45861400	Enhancers	Fetal Intestine Large	intestine
38	chr3:45857800-45858800	Weak transcription	Fetal Brain Female	brain
39	chr3:45857800-45859200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:45857800-45859800	Enhancers	Hela-S3	cervix
41	chr3:45857800-45860000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:45857800-45861200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:45857800-45861800	Enhancers	HSMM	muscle
44	chr3:45857800-45862800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr3:45857800-45863600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:45857800-45871600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:45858000-45858800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:45858000-45858800	Weak transcription	Liver	Liver
49	chr3:45858000-45859000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:45858000-45859800	Weak transcription	Ovary	ovary

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