Variant report

Variant	rs2439227
Chromosome Location	chr3:98559339-98559340
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1036674	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10935512	1.00[AMR][1000 genomes]
rs1095913	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095914	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1351496	1.00[AMR][1000 genomes]
rs1383908	1.00[AMR][1000 genomes]
rs1383911	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1440157	1.00[AMR][1000 genomes]
rs1531736	1.00[AMR][1000 genomes]
rs1600787	0.87[AFR][1000 genomes]
rs1600788	1.00[AMR][1000 genomes]
rs1822019	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1972432	1.00[AMR][1000 genomes]
rs2099738	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2119189	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2128053	1.00[AMR][1000 genomes]
rs2173598	1.00[AMR][1000 genomes]
rs2439230	1.00[AMR][1000 genomes]
rs2439233	0.87[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]
rs2454675	0.87[AFR][1000 genomes];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	0.87[AFR][1000 genomes]
rs4273318	1.00[AMR][1000 genomes]
rs4857107	1.00[AMR][1000 genomes]
rs5013928	1.00[AMR][1000 genomes]
rs6440232	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7373983	1.00[AMR][1000 genomes]
rs7626395	1.00[AMR][1000 genomes]
rs7630797	1.00[AMR][1000 genomes]
rs774549	0.85[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	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs974981	0.85[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:69 , 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	chr3:98545400-98561600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:98548800-98566600	Weak transcription	Adipose Nuclei	Adipose
12	chr3:98550200-98568600	Weak transcription	Thymus	Thymus
13	chr3:98550800-98561800	Weak transcription	HSMMtube	muscle
14	chr3:98551600-98562000	Weak transcription	Fetal Heart	heart
15	chr3:98552600-98566600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:98552600-98567000	Weak transcription	Fetal Kidney	kidney
17	chr3:98552800-98561400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:98552800-98566600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:98552800-98575800	Weak transcription	Pancreas	Pancrea
20	chr3:98552800-98578000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
22	chr3:98553000-98559400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:98553000-98559400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:98553000-98561400	Weak transcription	Fetal Lung	lung
25	chr3:98553000-98562400	Weak transcription	NHLF	lung
26	chr3:98553000-98563200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:98553000-98565800	Weak transcription	Ovary	ovary
28	chr3:98553000-98566800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:98553000-98566800	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:98553000-98567000	Weak transcription	Brain Germinal Matrix	brain
31	chr3:98553000-98575600	Weak transcription	Fetal Stomach	stomach
32	chr3:98553000-98576000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:98553000-98576200	Weak transcription	Left Ventricle	heart
34	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:98556600-98559600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:98557400-98560200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:98557800-98559800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:98557800-98559800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:98557800-98560000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:98557800-98560000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:98557800-98560200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr3:98558000-98562400	Strong transcription	NH-A	brain
43	chr3:98558200-98560000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:98558200-98560000	Genic enhancers	A549	lung
45	chr3:98558200-98560200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
46	chr3:98558200-98560200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:98558200-98560400	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr3:98558200-98560400	Strong transcription	HSMM	muscle
49	chr3:98558200-98561400	Strong transcription	Osteobl	bone
50	chr3:98558200-98566800	Weak transcription	Fetal Thymus	thymus

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