Variant report

Variant	rs828623
Chromosome Location	chr3:98546901-98546902
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	chr3:98542228..98544778-chr3:98545790..98547859,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	1.00[AMR][1000 genomes]
rs1383908	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	1.00[AMR][1000 genomes]
rs1600788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2099738	1.00[AMR][1000 genomes]
rs2119189	1.00[AMR][1000 genomes]
rs2128053	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2173598	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439235	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2448985	1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454690	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470828	1.00[AMR][1000 genomes]
rs2470839	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	1.00[AMR][1000 genomes]
rs2470856	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470858	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470866	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470883	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278375	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278378	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278384	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4273318	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	1.00[AMR][1000 genomes]
rs5013928	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs7373983	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626395	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828607	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828611	0.89[AFR][1000 genomes]
rs828619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	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:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
3	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:98534000-98552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:98534200-98552200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:98536000-98552600	Weak transcription	Pancreas	Pancrea
8	chr3:98536200-98594200	Weak transcription	HepG2	liver
9	chr3:98537000-98567000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:98537000-98592800	Weak transcription	K562	blood
11	chr3:98537400-98551200	Weak transcription	Fetal Heart	heart
12	chr3:98538200-98569200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:98538800-98548200	Weak transcription	Adipose Nuclei	Adipose
14	chr3:98538800-98552200	Weak transcription	Left Ventricle	heart
15	chr3:98541200-98552200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:98541200-98567000	Weak transcription	Liver	Liver
17	chr3:98541400-98565000	Weak transcription	HUVEC	blood vessel
18	chr3:98541600-98548400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:98542800-98551200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:98543000-98552400	Weak transcription	NHLF	lung
21	chr3:98543400-98552400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:98543400-98552400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:98543400-98552400	Weak transcription	Fetal Stomach	stomach
24	chr3:98543600-98551200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:98543600-98552200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:98543800-98548200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:98543800-98550000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:98543800-98551000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:98545000-98547000	Enhancers	Fetal Lung	lung
30	chr3:98545400-98552200	Weak transcription	Ovary	ovary
31	chr3:98545400-98552400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:98545400-98552400	Weak transcription	NHDF-Ad	bronchial
33	chr3:98545400-98561600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:98545600-98547800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:98545600-98548200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:98545600-98551200	Weak transcription	HSMM	muscle
37	chr3:98545600-98551600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:98545800-98551000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:98545800-98551200	Weak transcription	Osteobl	bone
40	chr3:98545800-98552200	Weak transcription	HMEC	breast
41	chr3:98546200-98550000	Weak transcription	NH-A	brain
42	chr3:98546400-98547400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:98546400-98550600	Weak transcription	HSMMtube	muscle
44	chr3:98546800-98550200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:98546800-98550400	Weak transcription	A549	lung
46	chr3:98546800-98551200	Weak transcription	NHEK	skin
47	chr3:98546800-98551400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:98546800-98552400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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