Variant report

Variant	rs2583980
Chromosome Location	chr4:90751109-90751110
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs13142587	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1372516	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1442146	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1442147	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1442149	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2028535	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2165614	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2583958	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583959	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583965	0.82[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583966	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2583967	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2583969	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2583970	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2583971	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583973	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583974	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583976	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2583977	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2583981	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583982	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583983	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583984	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583985	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583987	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2583988	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2583989	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2619343	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2619344	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2619345	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2619346	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2619348	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2619350	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619351	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619352	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619353	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619354	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2619358	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619359	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619360	0.94[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619361	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619362	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619363	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619364	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619366	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2619367	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2619370	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2619371	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619373	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2736995	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2736996	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2736997	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2736998	0.90[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2736999	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737000	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737001	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737003	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2737004	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2737005	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2737006	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2737008	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2737009	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2737012	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2737013	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2737014	0.95[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2737015	0.95[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2737016	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2737017	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2737018	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2737019	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2737022	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737023	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2737024	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2737033	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2737035	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs33965306	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs356163	0.91[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356184	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs356185	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs356187	0.90[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356189	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356192	0.84[CEU][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356195	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs356199	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67876224	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs986609	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs986610	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs990086	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs990087	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs990088	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90722200-90751800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:90730200-90757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:90730800-90757000	Weak transcription	Fetal Stomach	stomach
4	chr4:90735800-90755600	Weak transcription	Fetal Brain Male	brain
5	chr4:90738000-90755800	Weak transcription	Fetal Brain Female	brain
6	chr4:90738400-90756600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:90742800-90752200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:90743400-90753400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:90743400-90756600	Weak transcription	NHEK	skin
10	chr4:90743400-90757400	Weak transcription	Gastric	stomach
11	chr4:90743600-90754600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:90743800-90756600	Weak transcription	Ovary	ovary
13	chr4:90748800-90755600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:90750000-90751200	Enhancers	Primary T cells from cord blood	blood
15	chr4:90750000-90751400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:90750200-90751200	Enhancers	Primary B cells from cord blood	blood
17	chr4:90750200-90752000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr4:90750400-90751200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr4:90750400-90751200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr4:90750400-90751200	Active TSS	Brain Angular Gyrus	brain
21	chr4:90750400-90751400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:90750400-90751400	Flanking Active TSS	Dnd41	blood
23	chr4:90750400-90751400	Genic enhancers	HMEC	breast
24	chr4:90750400-90751400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr4:90750400-90751600	Genic enhancers	HUVEC	blood vessel
26	chr4:90750600-90751200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:90750600-90751200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:90750600-90751200	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr4:90750600-90751200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:90750600-90751200	Enhancers	GM12878-XiMat	blood
31	chr4:90750600-90751400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:90750600-90751400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:90750600-90751400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr4:90750600-90752600	Strong transcription	Fetal Lung	lung
35	chr4:90750800-90751200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr4:90750800-90751200	Active TSS	Primary hematopoietic stem cells	blood
37	chr4:90750800-90751200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr4:90750800-90751200	Enhancers	Thymus	Thymus
39	chr4:90750800-90751400	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr4:90751000-90751200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:90751000-90751200	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr4:90751000-90751400	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr4:90751000-90751400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr4:90751000-90751400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr4:90751000-90751400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:90751000-90751400	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr4:90751000-90751600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:90751000-90751600	Enhancers	Brain Substantia Nigra	brain
49	chr4:90751000-90751800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr4:90751000-90754000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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