Variant report

Variant	rs2488
Chromosome Location	chr3:120113286-120113287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1056928	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147693	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1147698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147699	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061630	1.00[JPT][hapmap]
rs13081675	1.00[JPT][hapmap]
rs13081694	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13096256	1.00[JPT][hapmap]
rs13097755	1.00[JPT][hapmap]
rs13100865	1.00[JPT][hapmap]
rs13709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1492272	1.00[JPT][hapmap]
rs1515577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17813772	1.00[JPT][hapmap]
rs1969356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029607	1.00[JPT][hapmap]
rs2030414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091726	1.00[JPT][hapmap]
rs2272515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4146299	1.00[JPT][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4676698	1.00[JPT][hapmap]
rs4676776	1.00[JPT][hapmap]
rs4676778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676781	1.00[JPT][hapmap]
rs4676782	1.00[JPT][hapmap]
rs4676783	1.00[JPT][hapmap]
rs6438575	1.00[JPT][hapmap]
rs869247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120103600-120113400	Weak transcription	Right Ventricle	heart
2	chr3:120107000-120114000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:120107000-120115200	Weak transcription	Spleen	Spleen
4	chr3:120107000-120118200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:120110000-120118200	Weak transcription	Esophagus	oesophagus
6	chr3:120111000-120114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:120111200-120113400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:120111200-120113400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:120111400-120115200	Weak transcription	A549	lung
10	chr3:120111400-120115400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:120111600-120113400	Weak transcription	Lung	lung
12	chr3:120111600-120114000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:120111600-120114800	Weak transcription	Fetal Intestine Small	intestine
14	chr3:120111800-120113400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:120111800-120113400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:120111800-120113400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:120111800-120113400	Weak transcription	Liver	Liver
18	chr3:120111800-120113400	Weak transcription	Placenta	Placenta
19	chr3:120111800-120115200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:120112000-120113600	Weak transcription	Brain Anterior Caudate	brain
21	chr3:120112000-120114600	Weak transcription	Fetal Brain Female	brain
22	chr3:120112000-120115400	Weak transcription	Brain Germinal Matrix	brain
23	chr3:120112000-120123600	Strong transcription	Osteobl	bone
24	chr3:120112000-120123800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:120112000-120132600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr3:120112200-120113800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:120112200-120123600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:120112200-120124000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:120112200-120124000	Strong transcription	HSMM	muscle
30	chr3:120112200-120127400	Strong transcription	Left Ventricle	heart
31	chr3:120112200-120130000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:120112200-120131400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:120112200-120132600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:120112400-120113800	Enhancers	Rectal Smooth Muscle	rectum
35	chr3:120112400-120114800	Genic enhancers	Colon Smooth Muscle	Colon
36	chr3:120112400-120123600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:120112400-120123800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:120112400-120123800	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr3:120112400-120129600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr3:120112400-120130200	Strong transcription	Adipose Nuclei	Adipose
41	chr3:120112400-120132600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:120112400-120132600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:120112400-120132600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:120112400-120132600	Strong transcription	HSMMtube	muscle
45	chr3:120112400-120132600	Strong transcription	NH-A	brain
46	chr3:120112400-120132600	Strong transcription	NHDF-Ad	bronchial
47	chr3:120112400-120132600	Strong transcription	NHLF	lung
48	chr3:120112600-120113800	Strong transcription	Fetal Stomach	stomach
49	chr3:120112600-120114400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:120112600-120115200	Weak transcription	Brain Inferior Temporal Lobe	brain

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