Variant report

Variant	rs1259327
Chromosome Location	chr3:120116922-120116923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1147682	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1147683	0.94[AMR][1000 genomes]
rs1147686	0.94[AMR][1000 genomes]
rs1147687	0.87[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs1147691	0.94[AMR][1000 genomes]
rs1147692	0.87[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs1147702	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1147704	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1147705	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1259290	0.86[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1259291	0.86[ASN][1000 genomes]
rs1259292	0.86[ASN][1000 genomes]
rs1259293	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1259294	0.81[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1259295	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259296	0.86[ASN][1000 genomes]
rs1259297	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1588890	0.84[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs1588891	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs1606872	0.94[AMR][1000 genomes]
rs1606873	0.94[AMR][1000 genomes]
rs1615793	0.95[AMR][1000 genomes]
rs1621291	0.87[CEU][hapmap]
rs1623323	0.94[AMR][1000 genomes]
rs1716840	0.87[CEU][hapmap]
rs1716846	0.94[AMR][1000 genomes]
rs1733325	0.94[AMR][1000 genomes]
rs1733327	0.94[AMR][1000 genomes]
rs1733329	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1733331	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1733353	0.94[AMR][1000 genomes]
rs1733354	0.94[AMR][1000 genomes]
rs2673704	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2700260	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2702156	0.87[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes]
rs2702158	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs2702164	0.94[AMR][1000 genomes]
rs2943754	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs6438576	1.00[YRI][hapmap]
rs6438578	1.00[YRI][hapmap]
rs787197	1.00[YRI][hapmap]
rs916509	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs916512	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs939500	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs950649	0.90[AMR][1000 genomes]
rs950650	0.94[AMR][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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120107000-120118200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:120110000-120118200	Weak transcription	Esophagus	oesophagus
3	chr3:120112000-120123600	Strong transcription	Osteobl	bone
4	chr3:120112000-120123800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:120112000-120132600	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr3:120112200-120123600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:120112200-120124000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:120112200-120124000	Strong transcription	HSMM	muscle
9	chr3:120112200-120127400	Strong transcription	Left Ventricle	heart
10	chr3:120112200-120130000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr3:120112200-120131400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:120112200-120132600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:120112400-120123600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:120112400-120123800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:120112400-120123800	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr3:120112400-120129600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr3:120112400-120130200	Strong transcription	Adipose Nuclei	Adipose
18	chr3:120112400-120132600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:120112400-120132600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:120112400-120132600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:120112400-120132600	Strong transcription	HSMMtube	muscle
22	chr3:120112400-120132600	Strong transcription	NH-A	brain
23	chr3:120112400-120132600	Strong transcription	NHDF-Ad	bronchial
24	chr3:120112400-120132600	Strong transcription	NHLF	lung
25	chr3:120112600-120122600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:120112600-120123000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:120112600-120130600	Strong transcription	Ovary	ovary
28	chr3:120112600-120131400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:120112600-120132400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:120112600-120132400	Strong transcription	Aorta	Aorta
31	chr3:120112600-120132600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:120112600-120132600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:120112600-120132800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:120112800-120123600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:120112800-120131200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:120112800-120132000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:120112800-120132600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:120112800-120132600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:120113200-120122600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:120113200-120122600	Strong transcription	HMEC	breast
41	chr3:120113200-120127400	Strong transcription	Fetal Muscle Leg	muscle
42	chr3:120113200-120132400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:120113200-120132600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:120113200-120132600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:120113200-120132600	Strong transcription	Fetal Kidney	kidney
46	chr3:120113200-120132600	Strong transcription	HUVEC	blood vessel
47	chr3:120113200-120133000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:120113400-120122400	Strong transcription	Lung	lung
49	chr3:120113400-120122600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:120113400-120126400	Strong transcription	Right Ventricle	heart

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