Variant report

Variant	rs6544890
Chromosome Location	chr2:46586114-46586115
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46567230..46569662-chr2:46585772..46587519,2	MCF-7	breast:
2	chr2:46581989..46584862-chr2:46585193..46588619,3	K562	blood:
3	chr2:46562482..46564557-chr2:46585775..46588142,2	K562	blood:

Variant related genes	Relation type
ENSG00000116016	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10191091	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1530631	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1530633	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1562452	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1562453	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2881324	0.80[ASN][1000 genomes]
rs3768730	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4953356	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953358	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953359	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544887	0.82[EUR][1000 genomes]
rs6544888	0.82[EUR][1000 genomes]
rs6544889	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6707241	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6735812	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6740096	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743991	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6756667	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7586141	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46568000-46596600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:46572600-46590600	Strong transcription	NHEK	skin
3	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
4	chr2:46573800-46591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:46574000-46586200	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:46574000-46589200	Strong transcription	Osteobl	bone
7	chr2:46574000-46589600	Strong transcription	A549	lung
8	chr2:46574200-46589600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:46574200-46590600	Strong transcription	Placenta Amnion	Placenta Amnion
10	chr2:46574400-46587400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:46574400-46590400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:46574800-46613000	Weak transcription	HSMM	muscle
14	chr2:46578600-46590400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:46578800-46590800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:46579400-46588000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:46579600-46587800	Weak transcription	Fetal Lung	lung
18	chr2:46580000-46587800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:46580000-46588600	Strong transcription	NHLF	lung
20	chr2:46580000-46589000	Strong transcription	Liver	Liver
21	chr2:46580000-46594600	Weak transcription	Psoas Muscle	Psoas
22	chr2:46580200-46588600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:46580400-46589600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr2:46580600-46589200	Weak transcription	Dnd41	blood
25	chr2:46580600-46589600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:46580600-46597200	Weak transcription	Fetal Heart	heart
27	chr2:46580800-46589800	Strong transcription	HUVEC	blood vessel
28	chr2:46581000-46586200	Genic enhancers	Right Ventricle	heart
29	chr2:46581000-46588000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:46581000-46589200	Strong transcription	Adipose Nuclei	Adipose
31	chr2:46581000-46589800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:46581200-46597000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:46581400-46589000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:46581800-46589400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:46581800-46589600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:46582800-46588000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:46582800-46589800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:46582800-46590200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr2:46583000-46586200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:46583000-46586200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:46583000-46586400	Strong transcription	Aorta	Aorta
42	chr2:46583000-46590400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr2:46583000-46591000	Weak transcription	Fetal Kidney	kidney
44	chr2:46583000-46591000	Strong transcription	Ovary	ovary
45	chr2:46583200-46586200	Strong transcription	HMEC	breast
46	chr2:46583200-46588400	Weak transcription	Primary T cells from cord blood	blood
47	chr2:46583200-46591000	Strong transcription	Gastric	stomach
48	chr2:46583600-46586200	Genic enhancers	HepG2	liver
49	chr2:46583600-46587400	Weak transcription	Right Atrium	heart
50	chr2:46583600-46587600	Strong transcription	Fetal Muscle Leg	muscle

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