Variant report

Variant	rs2493409
Chromosome Location	chr1:120512104-120512105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120511011..120512571-chr1:120512648..120514859,2	MCF-7	breast:
2	chr1:120506490..120508816-chr1:120511166..120513113,2	K562	blood:
3	chr1:120489170..120492877-chr1:120510169..120513121,3	K562	blood:
4	chr1:120505566..120508296-chr1:120511053..120512742,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs17024243	1.00[EUR][1000 genomes]
rs17024274	1.00[EUR][1000 genomes]
rs2453043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453045	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453054	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453057	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453060	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2493393	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2493395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2493397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2493399	1.00[EUR][1000 genomes]
rs2641341	1.00[EUR][1000 genomes]
rs2691751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2793828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2793924	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34996202	1.00[EUR][1000 genomes]
rs4274109	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59055697	1.00[EUR][1000 genomes]
rs60594933	1.00[EUR][1000 genomes]
rs6673881	1.00[EUR][1000 genomes]
rs6689706	1.00[EUR][1000 genomes]
rs6690032	1.00[EUR][1000 genomes]
rs6697236	1.00[EUR][1000 genomes]
rs74115097	1.00[EUR][1000 genomes]
rs74115360	1.00[EUR][1000 genomes]
rs74115365	1.00[EUR][1000 genomes]
rs7536072	1.00[EUR][1000 genomes]
rs7537153	1.00[EUR][1000 genomes]
rs7537385	1.00[EUR][1000 genomes]
rs7540526	1.00[EUR][1000 genomes]
rs835566	1.00[EUR][1000 genomes]
rs835567	1.00[EUR][1000 genomes]
rs835577	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1816057	chr1:120469050-120697156	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv1818054	chr1:120469050-120697156	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1844863	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv1850218	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv427730	chr1:120469050-120697156	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120468600-120532800	Weak transcription	Stomach Mucosa	stomach
2	chr1:120490000-120512400	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr1:120490000-120514400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:120490000-120517600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:120490200-120512600	Strong transcription	Primary T cells from cord blood	blood
6	chr1:120490200-120512600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:120490200-120521000	Strong transcription	Primary B cells from cord blood	blood
8	chr1:120490400-120512600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:120490800-120515000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:120491200-120538800	Weak transcription	Fetal Brain Male	brain
11	chr1:120493600-120512200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:120499400-120514600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:120500200-120515400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:120504600-120512200	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr1:120504600-120515000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:120504600-120517600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:120504800-120514000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:120505200-120512600	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr1:120505200-120515200	Strong transcription	Dnd41	blood
20	chr1:120505400-120512600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:120505400-120514600	Strong transcription	Thymus	Thymus
22	chr1:120505400-120514800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:120505600-120514600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:120505600-120514600	Strong transcription	Primary hematopoietic stem cells	blood
25	chr1:120506200-120512600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:120506400-120512200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:120506600-120512200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:120507200-120514200	Strong transcription	Fetal Kidney	kidney
29	chr1:120507800-120512200	Genic enhancers	Liver	Liver
30	chr1:120508000-120512400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:120508000-120514400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:120508000-120515800	Strong transcription	Fetal Stomach	stomach
33	chr1:120508000-120517800	Weak transcription	Psoas Muscle	Psoas
34	chr1:120508200-120512600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:120508200-120514600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:120508400-120515600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:120508400-120518600	Weak transcription	Fetal Brain Female	brain
38	chr1:120508600-120529800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:120508800-120517800	Weak transcription	Brain Angular Gyrus	brain
40	chr1:120508800-120524600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:120509000-120514000	Strong transcription	NH-A	brain
42	chr1:120509000-120516000	Weak transcription	Small Intestine	intestine
43	chr1:120509000-120533000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:120509200-120514400	Strong transcription	NHLF	lung
45	chr1:120509200-120515000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:120509400-120514600	Strong transcription	Fetal Lung	lung
47	chr1:120509600-120514600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:120509600-120515400	Weak transcription	Brain Substantia Nigra	brain
49	chr1:120509600-120520600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:120509600-120520600	Weak transcription	Right Ventricle	heart

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