Variant report

Variant	rs1259309
Chromosome Location	chr3:120179752-120179753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1123897	0.84[CHB][hapmap]
rs1147709	0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1147710	0.84[ASN][1000 genomes]
rs1147712	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147714	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147715	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147716	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147718	0.96[ASN][1000 genomes]
rs1147722	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1259311	0.84[CHB][hapmap]
rs1259312	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259315	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1259318	0.84[CHB][hapmap]
rs1259329	0.84[CHB][hapmap];0.81[YRI][hapmap]
rs1259331	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1259332	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1259334	0.84[CHB][hapmap]
rs1259336	0.84[CHB][hapmap]
rs1259337	0.84[CHB][hapmap]
rs1259338	0.84[CHB][hapmap]
rs1259456	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1259471	0.84[ASN][1000 genomes]
rs1259472	0.84[ASN][1000 genomes]
rs1259473	0.84[ASN][1000 genomes]
rs1262395	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1267675	0.84[CHB][hapmap]
rs1267693	0.88[ASN][1000 genomes]
rs1270209	0.84[CHB][hapmap]
rs1272257	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1520881	0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1716835	0.84[CHB][hapmap]
rs1733296	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs1733301	0.81[ASN][1000 genomes]
rs1733303	0.81[ASN][1000 genomes]
rs1733304	0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1733306	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1733307	0.81[ASN][1000 genomes]
rs1733319	0.84[CHB][hapmap]
rs2700262	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2702155	0.84[ASW][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs5000757	0.82[ASN][1000 genomes]
rs735138	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874478	0.81[ASN][1000 genomes]
rs874479	0.84[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs9631455	0.84[CHB][hapmap]
rs988924	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120170400-120190800	Weak transcription	Aorta	Aorta
2	chr3:120171800-120180600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:120177200-120180600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:120177600-120180400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:120178200-120180800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:120178200-120180800	Enhancers	NHLF	lung
7	chr3:120178200-120181200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:120178200-120181600	Enhancers	Right Atrium	heart
9	chr3:120178600-120180000	Enhancers	Fetal Muscle Leg	muscle
10	chr3:120178600-120180000	Enhancers	HSMMtube	muscle
11	chr3:120178600-120181200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:120178600-120181200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:120178800-120179800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:120178800-120179800	Enhancers	Fetal Kidney	kidney
15	chr3:120178800-120179800	Weak transcription	Left Ventricle	heart
16	chr3:120178800-120180000	Enhancers	Stomach Smooth Muscle	stomach
17	chr3:120178800-120180800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:120178800-120181200	Enhancers	Brain Germinal Matrix	brain
19	chr3:120179000-120179800	Enhancers	Brain Hippocampus Middle	brain
20	chr3:120179000-120180400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:120179000-120180600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:120179000-120180800	Enhancers	Fetal Brain Male	brain
23	chr3:120179200-120180600	Enhancers	NH-A	brain
24	chr3:120179200-120180800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:120179200-120181000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:120179200-120181400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:120179200-120181800	Enhancers	NHDF-Ad	bronchial
28	chr3:120179400-120179800	Enhancers	Colon Smooth Muscle	Colon
29	chr3:120179400-120180000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:120179400-120180200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:120179400-120180400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:120179600-120179800	Active TSS	Brain Anterior Caudate	brain
33	chr3:120179600-120180000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr3:120179600-120180000	Active TSS	Brain Angular Gyrus	brain
35	chr3:120179600-120180000	Active TSS	Brain Cingulate Gyrus	brain
36	chr3:120179600-120180000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:120179600-120180000	Active TSS	Brain Substantia Nigra	brain
38	chr3:120179600-120180000	Flanking Active TSS	Fetal Brain Female	brain
39	chr3:120179600-120180200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:120179600-120180200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr3:120179600-120180200	Enhancers	Rectal Smooth Muscle	rectum

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