Variant report

Variant	rs2454675
Chromosome Location	chr3:98575802-98575803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1036674	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1082401	0.81[AFR][1000 genomes]
rs10935512	1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	1.00[AMR][1000 genomes]
rs1383908	1.00[AMR][1000 genomes]
rs1383911	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1440157	1.00[AMR][1000 genomes]
rs1531736	1.00[AMR][1000 genomes]
rs1600787	0.83[AFR][1000 genomes]
rs1600788	1.00[AMR][1000 genomes]
rs1822019	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1972432	1.00[AMR][1000 genomes]
rs2099738	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2119189	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2128053	1.00[AMR][1000 genomes]
rs2173598	1.00[AMR][1000 genomes]
rs2439227	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439230	1.00[AMR][1000 genomes]
rs2439233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439234	1.00[AMR][1000 genomes]
rs2439235	1.00[AMR][1000 genomes]
rs2448985	1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes]
rs2454672	1.00[AMR][1000 genomes]
rs2454681	1.00[AMR][1000 genomes]
rs2454683	1.00[AMR][1000 genomes]
rs2454690	1.00[AMR][1000 genomes]
rs2470828	1.00[AMR][1000 genomes]
rs2470839	1.00[AMR][1000 genomes]
rs2470850	1.00[AMR][1000 genomes]
rs2470856	1.00[AMR][1000 genomes]
rs2470858	1.00[AMR][1000 genomes]
rs2470866	1.00[AMR][1000 genomes]
rs2470868	1.00[AMR][1000 genomes]
rs2470874	1.00[AMR][1000 genomes]
rs2470883	1.00[AMR][1000 genomes]
rs278375	1.00[AMR][1000 genomes]
rs278377	1.00[AMR][1000 genomes]
rs278378	1.00[AMR][1000 genomes]
rs278384	1.00[AMR][1000 genomes]
rs278385	1.00[AMR][1000 genomes]
rs278386	1.00[AMR][1000 genomes]
rs278389	1.00[AMR][1000 genomes]
rs2922213	1.00[AMR][1000 genomes]
rs2929488	0.83[AFR][1000 genomes]
rs4273318	1.00[AMR][1000 genomes]
rs4857107	1.00[AMR][1000 genomes]
rs5013928	1.00[AMR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs7373983	1.00[AMR][1000 genomes]
rs7626395	1.00[AMR][1000 genomes]
rs7630797	1.00[AMR][1000 genomes]
rs774549	0.80[AFR][1000 genomes]
rs828604	1.00[AMR][1000 genomes]
rs828606	1.00[AMR][1000 genomes]
rs828607	1.00[AMR][1000 genomes]
rs828619	1.00[AMR][1000 genomes]
rs828620	1.00[AMR][1000 genomes]
rs828622	1.00[AMR][1000 genomes]
rs828623	1.00[AMR][1000 genomes]
rs828624	1.00[AMR][1000 genomes]
rs866873	1.00[AMR][1000 genomes]
rs965757	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs974981	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98536200-98594200	Weak transcription	HepG2	liver
3	chr3:98537000-98592800	Weak transcription	K562	blood
4	chr3:98552800-98578000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
6	chr3:98553000-98576000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:98553000-98576200	Weak transcription	Left Ventricle	heart
8	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:98558200-98577200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:98559600-98576800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:98563600-98576000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:98567400-98578200	Weak transcription	Ovary	ovary
13	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:98567800-98576200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:98567800-98577000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:98568200-98578000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:98568400-98577200	Weak transcription	Dnd41	blood
18	chr3:98572400-98579200	Weak transcription	Brain Angular Gyrus	brain
19	chr3:98573000-98579200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:98574600-98582400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:98574800-98578200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:98575000-98576000	Strong transcription	Fetal Kidney	kidney
23	chr3:98575000-98576600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:98575000-98576800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:98575000-98577800	Strong transcription	Fetal Lung	lung
26	chr3:98575000-98579400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:98575200-98576000	Strong transcription	HMEC	breast
28	chr3:98575200-98576600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:98575200-98576600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:98575200-98577600	Weak transcription	NHLF	lung
31	chr3:98575200-98578000	ZNF genes & repeats	Brain Germinal Matrix	brain
32	chr3:98575200-98578000	ZNF genes & repeats	A549	lung
33	chr3:98575200-98578400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:98575200-98590200	Weak transcription	HSMMtube	muscle
35	chr3:98575400-98576000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:98575400-98576000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:98575400-98576000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
38	chr3:98575400-98577000	ZNF genes & repeats	Liver	Liver
39	chr3:98575400-98578000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr3:98575400-98578400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
41	chr3:98575400-98579200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:98575400-98583800	Weak transcription	HSMM	muscle
43	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:98575600-98576200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:98575600-98576600	ZNF genes & repeats	Adipose Nuclei	Adipose
46	chr3:98575600-98577200	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr3:98575600-98577400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
48	chr3:98575600-98577400	Weak transcription	NHEK	skin
49	chr3:98575600-98578200	ZNF genes & repeats	Fetal Stomach	stomach
50	chr3:98575600-98579000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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