Variant report

Variant	rs6544888
Chromosome Location	chr2:46577265-46577266
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46569601..46571271-chr2:46576825..46579452,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10191091	0.96[CEU][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11675232	0.80[CEU][hapmap]
rs11692911	0.80[CEU][hapmap]
rs12467821	0.80[CEU][hapmap]
rs1530631	0.92[CEU][hapmap]
rs1530633	0.96[CEU][hapmap]
rs1562452	1.00[CEU][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1562453	0.88[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2881324	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768730	0.88[CEU][hapmap]
rs4953356	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4953358	0.92[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4953359	0.92[CEU][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6544887	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544889	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6544890	0.82[EUR][1000 genomes]
rs6707241	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6724065	0.89[EUR][1000 genomes]
rs6735812	0.92[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6740096	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6743991	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6756667	0.92[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7568285	0.88[CEU][hapmap]
rs7586141	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7594912	0.88[CEU][hapmap]

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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46563800-46579000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:46564600-46578800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:46566600-46579200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:46567400-46584600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:46568000-46596600	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:46570200-46584800	Weak transcription	Small Intestine	intestine
7	chr2:46572000-46584600	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:46572200-46577600	Weak transcription	Fetal Lung	lung
9	chr2:46572400-46583200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:46572600-46578800	Enhancers	Fetal Thymus	thymus
11	chr2:46572600-46590600	Strong transcription	NHEK	skin
12	chr2:46572800-46577400	Weak transcription	NHDF-Ad	bronchial
13	chr2:46573200-46577600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr2:46573200-46584200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
16	chr2:46573400-46577600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:46573400-46583000	Weak transcription	Ovary	ovary
18	chr2:46573600-46583600	Weak transcription	Stomach Mucosa	stomach
19	chr2:46573800-46591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:46574000-46578200	Strong transcription	NHLF	lung
21	chr2:46574000-46578800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr2:46574000-46578800	Genic enhancers	Adipose Nuclei	Adipose
23	chr2:46574000-46586200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:46574000-46589200	Strong transcription	Osteobl	bone
25	chr2:46574000-46589600	Strong transcription	A549	lung
26	chr2:46574200-46577600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:46574200-46578600	Enhancers	Thymus	Thymus
28	chr2:46574200-46589600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:46574200-46590600	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr2:46574400-46577400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:46574400-46578600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:46574400-46579600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:46574400-46580000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:46574400-46587400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:46574400-46590400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:46574600-46577400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:46574600-46578200	Strong transcription	Fetal Stomach	stomach
38	chr2:46574600-46578600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr2:46574600-46578800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:46574800-46578400	Strong transcription	Fetal Intestine Large	intestine
42	chr2:46574800-46578600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr2:46574800-46613000	Weak transcription	HSMM	muscle
44	chr2:46575000-46577800	Enhancers	Dnd41	blood
45	chr2:46575000-46578600	Weak transcription	GM12878-XiMat	blood
46	chr2:46575400-46577800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:46575400-46578000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:46575400-46578400	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:46575400-46578800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:46575400-46581800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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