Variant report

Variant	rs2454690
Chromosome Location	chr3:98561773-98561774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98561160..98564034-chr3:98567276..98569600,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383908	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1600788	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	0.86[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	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2133575	0.85[AFR][1000 genomes]
rs2173598	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439232	1.00[ASN][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439235	0.95[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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470828	1.00[AMR][1000 genomes]
rs2470839	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	1.00[AMR][1000 genomes]
rs2470856	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470858	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2470866	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470883	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470884	0.85[AFR][1000 genomes]
rs278375	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278378	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278384	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4273318	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	1.00[AMR][1000 genomes]
rs5013928	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440189	0.82[AFR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs6795351	0.82[AFR][1000 genomes]
rs7373983	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626395	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828607	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828611	0.83[AFR][1000 genomes]
rs828619	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828623	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	1.00[AMR][1000 genomes]
rs996199	0.85[AFR][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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:98536200-98594200	Weak transcription	HepG2	liver
5	chr3:98537000-98567000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:98537000-98592800	Weak transcription	K562	blood
7	chr3:98538200-98569200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:98541200-98567000	Weak transcription	Liver	Liver
9	chr3:98541400-98565000	Weak transcription	HUVEC	blood vessel
10	chr3:98548800-98566600	Weak transcription	Adipose Nuclei	Adipose
11	chr3:98550200-98568600	Weak transcription	Thymus	Thymus
12	chr3:98550800-98561800	Weak transcription	HSMMtube	muscle
13	chr3:98551600-98562000	Weak transcription	Fetal Heart	heart
14	chr3:98552600-98566600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:98552600-98567000	Weak transcription	Fetal Kidney	kidney
16	chr3:98552800-98566600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:98552800-98575800	Weak transcription	Pancreas	Pancrea
18	chr3:98552800-98578000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
20	chr3:98553000-98562400	Weak transcription	NHLF	lung
21	chr3:98553000-98563200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:98553000-98565800	Weak transcription	Ovary	ovary
23	chr3:98553000-98566800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:98553000-98566800	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:98553000-98567000	Weak transcription	Brain Germinal Matrix	brain
26	chr3:98553000-98575600	Weak transcription	Fetal Stomach	stomach
27	chr3:98553000-98576000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:98553000-98576200	Weak transcription	Left Ventricle	heart
29	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:98558000-98562400	Strong transcription	NH-A	brain
31	chr3:98558200-98566800	Weak transcription	Fetal Thymus	thymus
32	chr3:98558200-98569400	Weak transcription	Fetal Intestine Large	intestine
33	chr3:98558200-98569600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:98558200-98577200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:98558400-98566400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:98558400-98568800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:98558800-98567000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:98559000-98567000	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:98559000-98569000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:98559600-98576800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:98559800-98565800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:98559800-98566800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:98559800-98567000	Weak transcription	Dnd41	blood
44	chr3:98559800-98569400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:98560000-98563400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:98560000-98564600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:98560000-98566600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:98560000-98566800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:98560000-98575600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:98560200-98562800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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