Variant report

Variant	rs2293659
Chromosome Location	chr12:59267701-59267702
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59265300..59268066-chr12:59282069..59283994,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10877178	0.82[CHB][hapmap]
rs10877180	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11172711	0.83[AMR][1000 genomes]
rs11172717	0.88[AMR][1000 genomes]
rs11172727	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11172730	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172731	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172737	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172739	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172742	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172759	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172771	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11172774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172791	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172795	0.82[JPT][hapmap]
rs11172797	0.85[JPT][hapmap]
rs1148531	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11514001	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11514217	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11514219	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11514220	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11514221	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11520079	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11520080	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11520081	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11520082	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11520084	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12366986	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12367092	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12367116	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12367975	0.83[AMR][1000 genomes]
rs12368328	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12369527	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12370599	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12371811	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12372281	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17121454	0.83[AMR][1000 genomes]
rs17121505	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17121548	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17121569	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17121576	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17121582	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17617428	0.85[JPT][hapmap]
rs2279718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74099636	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59253000-59270200	Weak transcription	Fetal Brain Male	brain
2	chr12:59254600-59268600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:59257000-59270800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:59259200-59270200	Strong transcription	HMEC	breast
5	chr12:59260400-59270200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:59260600-59284200	Strong transcription	HUVEC	blood vessel
7	chr12:59261400-59270800	Strong transcription	Liver	Liver
8	chr12:59261400-59284200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr12:59261600-59284200	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr12:59261800-59270200	Strong transcription	HSMM	muscle
11	chr12:59261800-59275000	Strong transcription	Fetal Lung	lung
12	chr12:59261800-59280800	Strong transcription	Fetal Intestine Large	intestine
13	chr12:59262600-59268400	Weak transcription	Hela-S3	cervix
14	chr12:59262600-59269000	Weak transcription	Stomach Mucosa	stomach
15	chr12:59262600-59272400	Weak transcription	Fetal Heart	heart
16	chr12:59262600-59295000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:59262800-59268600	Weak transcription	Spleen	Spleen
18	chr12:59263000-59276400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:59263200-59270400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr12:59263200-59277000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:59263400-59267800	Weak transcription	Small Intestine	intestine
22	chr12:59263400-59270600	Strong transcription	A549	lung
23	chr12:59263400-59271200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:59263400-59281400	Strong transcription	NHEK	skin
25	chr12:59263600-59278800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:59264200-59274800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:59264400-59268600	Weak transcription	HepG2	liver
28	chr12:59264400-59274600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:59264800-59268200	Weak transcription	Fetal Brain Female	brain
30	chr12:59264800-59268600	Weak transcription	Brain Angular Gyrus	brain
31	chr12:59264800-59284200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr12:59265000-59277200	Weak transcription	GM12878-XiMat	blood
33	chr12:59265200-59271000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:59265400-59269400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:59265400-59275400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr12:59265400-59284200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:59265600-59271200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:59265600-59276200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:59265800-59270800	Strong transcription	NHLF	lung
40	chr12:59265800-59275800	Strong transcription	Fetal Kidney	kidney
41	chr12:59266000-59268800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:59266000-59282000	Strong transcription	Adipose Nuclei	Adipose
43	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
44	chr12:59266200-59270600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:59266200-59274800	Strong transcription	Colon Smooth Muscle	Colon
46	chr12:59266200-59278600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:59266200-59284000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr12:59266400-59268200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:59266400-59268800	Strong transcription	Brain Cingulate Gyrus	brain
50	chr12:59266400-59269000	Strong transcription	Esophagus	oesophagus

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