Variant report

Variant	rs16839330
Chromosome Location	chr2:133425860-133425861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:133424851..133426510-chr2:133433798..133435548,2	MCF-7	breast:
2	chr2:133425043..133426903-chr2:133429908..133431486,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10439200	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10928434	1.00[ASN][1000 genomes]
rs11884351	1.00[ASN][1000 genomes]
rs13386133	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13392087	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13431116	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13431416	1.00[ASN][1000 genomes]
rs16839091	0.82[ASW][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16840001	1.00[ASN][1000 genomes]
rs2320152	1.00[JPT][hapmap]
rs56821454	1.00[ASN][1000 genomes]
rs57381356	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57457802	1.00[ASN][1000 genomes]
rs57987015	1.00[ASN][1000 genomes]
rs59679606	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60981588	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6430372	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6719585	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6728913	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73955766	1.00[EUR][1000 genomes]
rs73955769	1.00[ASN][1000 genomes]
rs73955770	1.00[ASN][1000 genomes]
rs73955772	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955775	1.00[ASN][1000 genomes]
rs73955778	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955780	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955781	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73955782	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73955783	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73957619	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73957621	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7560906	1.00[ASN][1000 genomes]
rs7561232	1.00[ASN][1000 genomes]
rs7562087	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7565263	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7568136	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7570026	1.00[ASN][1000 genomes]
rs7579800	1.00[EUR][1000 genomes]
rs7586082	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589749	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7591904	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7595948	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7596374	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7603184	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7606118	1.00[JPT][hapmap];1.00[ASN][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	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers 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	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv875138	chr2:133410921-133761794	Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133404000-133426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:133410000-133426200	Weak transcription	Osteobl	bone
3	chr2:133414200-133426000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:133424600-133427000	Flanking Active TSS	HUVEC	blood vessel
5	chr2:133424800-133426000	Bivalent Enhancer	Fetal Stomach	stomach
6	chr2:133425200-133426000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr2:133425200-133426200	Enhancers	Lung	lung
8	chr2:133425200-133426600	Bivalent Enhancer	Fetal Heart	heart
9	chr2:133425400-133426000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:133425400-133426400	Bivalent Enhancer	Fetal Lung	lung
11	chr2:133425400-133426600	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:133425400-133429200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr2:133425600-133426000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
14	chr2:133425600-133426000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:133425600-133426000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr2:133425600-133426000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:133425600-133426000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:133425600-133426000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
19	chr2:133425600-133426000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:133425600-133426000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:133425600-133426000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
22	chr2:133425600-133426000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
23	chr2:133425600-133426000	Flanking Active TSS	NH-A	brain
24	chr2:133425600-133427200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:133425600-133427600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:133425800-133426000	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:133425800-133426000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr2:133425800-133426000	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr2:133425800-133426000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
30	chr2:133425800-133426000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:133425800-133426000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr2:133425800-133426000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
33	chr2:133425800-133426200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:133425800-133426200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:133425800-133426200	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr2:133425800-133426200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
37	chr2:133425800-133426400	Flanking Active TSS	Fetal Brain Female	brain
38	chr2:133425800-133426400	Bivalent Enhancer	NHLF	lung
39	chr2:133425800-133426600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:133425800-133426600	Active TSS	Brain Substantia Nigra	brain
41	chr2:133425800-133426600	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr2:133425800-133426800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
43	chr2:133425800-133426800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:133425800-133426800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:133425800-133427600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:133425800-133429000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
47	chr2:133425800-133429200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
48	chr2:133425800-133429200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr2:133425800-133429200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:133425800-133429200	Active TSS	Fetal Kidney	kidney

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