Variant report

Variant	rs6775999
Chromosome Location	chr3:43021383-43021384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43020888..43021726-chr6:43395171..43396067,2	HCT-116	colon:
2	chr3:42843694..42846057-chr3:43021283..43022980,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124574	Chromatin interaction
ENSG00000181061	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10470680	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129987	0.82[EUR][1000 genomes]
rs11129988	0.82[EUR][1000 genomes]
rs1392319	1.00[ASN][1000 genomes]
rs1403525	1.00[ASN][1000 genomes]
rs17074894	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238972	1.00[ASN][1000 genomes]
rs1816227	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28378297	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601753	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655956	1.00[ASN][1000 genomes]
rs28673478	1.00[ASN][1000 genomes]
rs3915020	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489117	1.00[ASN][1000 genomes]
rs526511	0.83[EUR][1000 genomes]
rs530842	1.00[ASN][1000 genomes]
rs534284	1.00[ASN][1000 genomes]
rs542394	0.84[EUR][1000 genomes]
rs545023	0.84[EUR][1000 genomes]
rs551658	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604393	1.00[ASN][1000 genomes]
rs60616619	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61004728	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615462	0.82[EUR][1000 genomes]
rs617014	1.00[ASN][1000 genomes]
rs619660	0.82[EUR][1000 genomes]
rs62248962	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249006	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249007	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249008	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249009	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249011	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249013	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249014	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249015	0.86[EUR][1000 genomes]
rs62249016	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249584	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638602	0.83[EUR][1000 genomes]
rs649682	0.83[EUR][1000 genomes]
rs651899	1.00[ASN][1000 genomes]
rs6763762	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773223	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678310	1.00[ASN][1000 genomes]
rs6798412	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798520	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs680967	1.00[ASN][1000 genomes]
rs681341	1.00[ASN][1000 genomes]
rs6865	1.00[ASN][1000 genomes]
rs73075297	1.00[ASN][1000 genomes]
rs73075301	1.00[ASN][1000 genomes]
rs73077208	1.00[ASN][1000 genomes]
rs73077214	1.00[ASN][1000 genomes]
rs73077238	1.00[ASN][1000 genomes]
rs73087348	1.00[ASN][1000 genomes]
rs735320	1.00[ASN][1000 genomes]
rs73832423	1.00[ASN][1000 genomes]
rs73832424	1.00[ASN][1000 genomes]
rs7617715	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641452	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644923	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834183	0.83[EUR][1000 genomes]
rs834579	0.82[EUR][1000 genomes]
rs834584	0.83[EUR][1000 genomes]
rs834699	0.83[EUR][1000 genomes]
rs9311330	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311331	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808932	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815609	1.00[ASN][1000 genomes]
rs9816391	1.00[ASN][1000 genomes]
rs9824700	1.00[ASN][1000 genomes]
rs9828785	1.00[ASN][1000 genomes]
rs9832875	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9833284	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837761	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840349	1.00[ASN][1000 genomes]
rs9852930	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858270	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862469	1.00[ASN][1000 genomes]
rs9870478	1.00[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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43020200-43021400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr3:43020200-43022000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:43020200-43022200	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:43020200-43022200	Active TSS	Rectal Smooth Muscle	rectum
5	chr3:43020400-43021400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:43020400-43021400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:43020400-43021400	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:43020400-43021400	Active TSS	Aorta	Aorta
9	chr3:43020400-43021600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:43020400-43021600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:43020400-43021600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
12	chr3:43020400-43021600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
13	chr3:43020400-43021600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:43020400-43021600	Bivalent/Poised TSS	Fetal Kidney	kidney
15	chr3:43020400-43021600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr3:43020400-43021600	Bivalent/Poised TSS	NHDF-Ad	bronchial
17	chr3:43020400-43021800	Active TSS	Colon Smooth Muscle	Colon
18	chr3:43020400-43022000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
19	chr3:43020400-43022200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:43020400-43022400	Active TSS	Brain Substantia Nigra	brain
21	chr3:43020400-43022800	Active TSS	Brain Anterior Caudate	brain
22	chr3:43020600-43021400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:43020600-43021400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:43020600-43021400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr3:43020600-43021400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:43020600-43021400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:43020600-43021400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:43020600-43021400	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr3:43020600-43021400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:43020600-43021400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:43020600-43021400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:43020600-43021400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:43020600-43021400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:43020600-43021400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
35	chr3:43020600-43021400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr3:43020600-43021400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr3:43020600-43021400	Active TSS	Left Ventricle	heart
38	chr3:43020600-43021400	Bivalent/Poised TSS	A549	lung
39	chr3:43020600-43021400	Bivalent/Poised TSS	HSMM	muscle
40	chr3:43020600-43021400	Bivalent/Poised TSS	Osteobl	bone
41	chr3:43020600-43021600	Active TSS	H9 Cell Line	embryonic stem cell
42	chr3:43020600-43021600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr3:43020600-43021600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr3:43020600-43021600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr3:43020600-43021600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
46	chr3:43020600-43021600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
47	chr3:43020600-43021600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
48	chr3:43020600-43021600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:43020600-43021600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
50	chr3:43020600-43021600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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