Variant report

Variant	rs1590979
Chromosome Location	chr9:2559492-2559493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1015469	0.89[JPT][hapmap]
rs10738706	0.89[JPT][hapmap]
rs10738707	0.81[ASN][1000 genomes]
rs10757513	0.89[JPT][hapmap]
rs10812242	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1360465	0.86[CHB][hapmap]
rs1537191	0.88[JPT][hapmap]
rs1571815	0.89[JPT][hapmap]
rs1598197	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs1707299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17488507	0.86[CHB][hapmap]
rs2183736	0.89[JPT][hapmap]
rs2297350	0.89[JPT][hapmap]
rs2492589	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3953850	0.86[JPT][hapmap]
rs4740687	0.89[JPT][hapmap]
rs494035	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs516289	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs541062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541759	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542859	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs543117	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543669	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580571	0.83[ASN][1000 genomes]
rs581859	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs609420	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626845	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656790	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675381	0.83[ASN][1000 genomes]
rs685878	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693007	0.85[ASN][1000 genomes]
rs693934	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852929	0.83[ASN][1000 genomes]
rs7859598	0.89[JPT][hapmap]
rs7860538	0.88[CHB][hapmap]
rs9298875	0.81[JPT][hapmap]
rs944548	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh 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	39 gene(s)	inside rSNPs	diseases
3	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS 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	12 gene(s)	inside rSNPs	diseases
6	nsv466081	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv613132	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv892066	chr9:2397564-2589739	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1033424	chr9:2508296-2575408	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1029876	chr9:2526760-2633562	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv892068	chr9:2543888-2589739	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2558400-2560000	Enhancers	Fetal Heart	heart
2	chr9:2558400-2561200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:2558800-2560800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:2558800-2561000	Enhancers	Fetal Lung	lung
5	chr9:2559000-2559800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr9:2559000-2560200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr9:2559000-2560200	Enhancers	Brain Hippocampus Middle	brain
8	chr9:2559000-2560400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:2559000-2560400	Flanking Active TSS	A549	lung
10	chr9:2559000-2560600	Enhancers	HMEC	breast
11	chr9:2559000-2560800	Enhancers	Fetal Stomach	stomach
12	chr9:2559000-2561200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:2559200-2559600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr9:2559200-2559600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr9:2559200-2559600	Enhancers	Aorta	Aorta
16	chr9:2559200-2559600	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr9:2559200-2559600	Flanking Active TSS	HSMM	muscle
18	chr9:2559200-2559800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr9:2559200-2559800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr9:2559200-2559800	Enhancers	Colon Smooth Muscle	Colon
21	chr9:2559200-2560000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:2559200-2560000	Flanking Active TSS	Osteobl	bone
23	chr9:2559200-2560200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:2559200-2560200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr9:2559200-2560200	Enhancers	Hela-S3	cervix
26	chr9:2559200-2560200	Enhancers	NHEK	skin
27	chr9:2559200-2560400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:2559200-2560400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:2559200-2560400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:2559200-2560400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr9:2559200-2560400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:2559200-2560400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:2559200-2560400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:2559200-2560400	Enhancers	Brain Cingulate Gyrus	brain
35	chr9:2559200-2560400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr9:2559200-2560400	Enhancers	Fetal Muscle Trunk	muscle
37	chr9:2559200-2560400	Enhancers	Gastric	stomach
38	chr9:2559200-2560400	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr9:2559200-2560400	Enhancers	NHDF-Ad	bronchial
40	chr9:2559200-2560600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr9:2559200-2560600	Enhancers	Brain Angular Gyrus	brain
42	chr9:2559200-2560600	Enhancers	Fetal Brain Male	brain
43	chr9:2559200-2560600	Enhancers	HSMMtube	muscle
44	chr9:2559200-2560800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:2559200-2560800	Enhancers	Lung	lung
46	chr9:2559200-2560800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr9:2559200-2561000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr9:2559200-2561000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:2559200-2561000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:2559200-2561000	Enhancers	Fetal Muscle Leg	muscle

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