Variant report

Variant	rs62154552
Chromosome Location	chr2:98459149-98459150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs55853292	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55887737	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58415781	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59444417	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59752876	0.80[EUR][1000 genomes]
rs61363543	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62154508	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62154513	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62154516	0.85[EUR][1000 genomes]
rs62154549	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62154553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154555	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154556	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154558	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62156482	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62156488	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62156507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62156508	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62156509	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62156514	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62157630	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73960435	0.80[EUR][1000 genomes]
rs7420897	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7575922	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7606272	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98405800-98459600	Weak transcription	Stomach Mucosa	stomach
2	chr2:98406400-98469200	Weak transcription	A549	lung
3	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
4	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
5	chr2:98424000-98475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:98424200-98461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:98425600-98461000	Weak transcription	Brain Germinal Matrix	brain
8	chr2:98428000-98466600	Weak transcription	K562	blood
9	chr2:98428600-98461200	Weak transcription	Fetal Brain Male	brain
10	chr2:98428600-98464600	Weak transcription	HSMMtube	muscle
11	chr2:98428800-98485000	Weak transcription	NHLF	lung
12	chr2:98429000-98470600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:98430000-98467800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:98431000-98466400	Weak transcription	NH-A	brain
15	chr2:98434200-98484000	Weak transcription	NHDF-Ad	bronchial
16	chr2:98434400-98466400	Weak transcription	Brain Substantia Nigra	brain
17	chr2:98434400-98485800	Weak transcription	Lung	lung
18	chr2:98445200-98459800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:98445800-98460000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:98446000-98460200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:98446000-98475000	Weak transcription	Gastric	stomach
22	chr2:98447400-98465400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:98447600-98461200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:98447800-98461200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:98447800-98466200	Weak transcription	Psoas Muscle	Psoas
26	chr2:98447800-98479600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:98447800-98502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:98448000-98461200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:98449600-98482000	Weak transcription	Fetal Kidney	kidney
30	chr2:98450600-98459600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:98450600-98460000	Strong transcription	Primary B cells from cord blood	blood
32	chr2:98451800-98466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:98452400-98459400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:98453200-98459800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:98454200-98459400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:98454400-98460000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:98455400-98459400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:98455400-98459400	Strong transcription	GM12878-XiMat	blood
39	chr2:98455400-98459600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:98455400-98459800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:98456000-98459200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:98456000-98459400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:98456000-98459400	Strong transcription	HMEC	breast
44	chr2:98456000-98459600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:98456000-98459800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:98456000-98459800	Strong transcription	Primary T cells from cord blood	blood
47	chr2:98456000-98459800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr2:98456000-98460000	Strong transcription	HSMM	muscle
49	chr2:98456000-98460200	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:98456200-98459800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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