Variant report

Variant	rs2782417
Chromosome Location	chr9:27110480-27110481
allele	G/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:29)

rs_ID	r²[population]
rs16911095	1.00[EUR][1000 genomes]
rs1762074	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2782414	1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2782418	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2782429	0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2782431	1.00[EUR][1000 genomes]
rs482271	1.00[EUR][1000 genomes]
rs529941	1.00[EUR][1000 genomes]
rs581470	1.00[EUR][1000 genomes]
rs596496	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs602255	1.00[EUR][1000 genomes]
rs610646	1.00[EUR][1000 genomes]
rs613009	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs615316	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs615532	0.82[AFR][1000 genomes]
rs615636	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs615908	0.89[AFR][1000 genomes]
rs629138	1.00[EUR][1000 genomes]
rs629582	1.00[EUR][1000 genomes]
rs653773	1.00[EUR][1000 genomes]
rs672470	1.00[EUR][1000 genomes]
rs674459	1.00[EUR][1000 genomes]
rs7390769	0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7390770	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7390781	1.00[EUR][1000 genomes]
rs7390786	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7390795	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7390806	0.81[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7390815	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27108600-27111000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:27108800-27110600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr9:27108800-27111600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr9:27108800-27111800	Active TSS	Right Atrium	heart
5	chr9:27108800-27112000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:27109000-27110600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr9:27109000-27110600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:27109000-27111000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:27109000-27111200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:27109000-27111400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr9:27109000-27111600	Active TSS	Fetal Intestine Small	intestine
12	chr9:27109000-27111600	Active TSS	Psoas Muscle	Psoas
13	chr9:27109000-27111600	Active TSS	Right Ventricle	heart
14	chr9:27109000-27111800	Active TSS	Fetal Kidney	kidney
15	chr9:27109000-27112200	Active TSS	Left Ventricle	heart
16	chr9:27109000-27112200	Active TSS	Lung	lung
17	chr9:27109000-27112600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr9:27109200-27110800	Active TSS	Fetal Muscle Leg	muscle
19	chr9:27109200-27111400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr9:27109400-27111400	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr9:27109600-27110600	Active TSS	Ovary	ovary
22	chr9:27109600-27111000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:27109600-27111200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:27109600-27111200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:27109600-27111200	Active TSS	NH-A	brain
26	chr9:27109600-27111400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr9:27109600-27111400	Active TSS	Fetal Stomach	stomach
28	chr9:27109600-27112400	Active TSS	Adipose Nuclei	Adipose
29	chr9:27109600-27117600	Weak transcription	HSMMtube	muscle
30	chr9:27109600-27117800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:27109800-27110800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:27109800-27111000	Active TSS	Fetal Intestine Large	intestine
33	chr9:27109800-27111000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr9:27109800-27111600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:27109800-27111600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:27109800-27117600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr9:27110000-27111000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:27110000-27111200	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr9:27110000-27111200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr9:27110000-27111200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:27110200-27111200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:27110200-27111400	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr9:27110400-27110600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr9:27110400-27110600	Enhancers	Primary hematopoietic stem cells	blood
45	chr9:27110400-27110600	Active TSS	HUVEC	blood vessel
46	chr9:27110400-27110600	Flanking Active TSS	Osteobl	bone
47	chr9:27110400-27110800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:27110400-27111000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr9:27110400-27122000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:27110400-27123200	Weak transcription	Fetal Lung	lung

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