Variant report

Variant	rs56804721
Chromosome Location	chr3:159978679-159978680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11929258	1.00[EUR][1000 genomes]
rs12106837	1.00[EUR][1000 genomes]
rs12107576	1.00[EUR][1000 genomes]
rs16831149	1.00[ASN][1000 genomes]
rs2275150	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278848	1.00[EUR][1000 genomes]
rs3773370	1.00[EUR][1000 genomes]
rs56992472	1.00[EUR][1000 genomes]
rs57094479	1.00[EUR][1000 genomes]
rs57310422	1.00[EUR][1000 genomes]
rs58993492	1.00[EUR][1000 genomes]
rs59308952	1.00[EUR][1000 genomes]
rs60535227	1.00[EUR][1000 genomes]
rs62272180	0.83[AFR][1000 genomes]
rs6441309	1.00[EUR][1000 genomes]
rs6441310	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764227	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773833	1.00[EUR][1000 genomes]
rs6773856	1.00[EUR][1000 genomes]
rs6793718	1.00[EUR][1000 genomes]
rs6802789	1.00[EUR][1000 genomes]
rs6808628	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154538	0.90[ASN][1000 genomes]
rs73875248	1.00[ASN][1000 genomes]
rs7635305	1.00[EUR][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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159971400-160035800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:159971800-159986200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:159971800-160009600	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:159972400-159984800	Weak transcription	Ovary	ovary
5	chr3:159972600-160009400	Weak transcription	Fetal Stomach	stomach
6	chr3:159972800-159999000	Weak transcription	Aorta	Aorta
7	chr3:159973200-159984200	Weak transcription	Thymus	Thymus
8	chr3:159973400-159994600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:159974000-159984400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:159974200-159992000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
12	chr3:159974400-159984600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:159974600-159991600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:159974600-159992200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:159974600-159999600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:159974800-159984600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:159974800-160014400	Weak transcription	HSMM	muscle
18	chr3:159975000-159991600	Weak transcription	Dnd41	blood
19	chr3:159975000-160025600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:159975000-160028000	Weak transcription	Brain Anterior Caudate	brain
21	chr3:159975000-160034200	Weak transcription	Fetal Intestine Large	intestine
22	chr3:159975200-159980600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:159975200-159994400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:159975400-159993800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:159975600-160009600	Weak transcription	Fetal Intestine Small	intestine
27	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:159976400-159984600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:159976600-159986000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:159976600-159994400	Weak transcription	Primary B cells from cord blood	blood
32	chr3:159976600-159995800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:159976800-159984800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:159977000-159984200	Weak transcription	Fetal Thymus	thymus
35	chr3:159977400-159979000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:159977400-159985200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:159977600-159979600	Weak transcription	Primary T cells from cord blood	blood
38	chr3:159977600-159984800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr3:159977600-159996000	Weak transcription	Left Ventricle	heart
40	chr3:159977800-159990600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:159977800-160014400	Weak transcription	NHDF-Ad	bronchial
42	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:159978000-159979000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:159978200-159978800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:159978200-159978800	Active TSS	Right Atrium	heart
46	chr3:159978200-159994400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:159978400-159978800	Active TSS	Adipose Nuclei	Adipose
48	chr3:159978600-159978800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:159978600-159978800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:159978600-159978800	Flanking Active TSS	Liver	Liver

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