Variant report

Variant	rs2279718
Chromosome Location	chr12:59270333-59270334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:59270042-59270450	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59268786..59271199-chr12:59312265..59313984,3	MCF-7	breast:

Variant related genes	Relation type
LRIG3	TF binding region
ENSG00000139263	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1020031	0.83[TSI][hapmap]
rs10877178	0.82[CHB][hapmap]
rs10877180	1.00[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs10877182	0.88[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs10877183	0.85[GIH][hapmap];0.83[TSI][hapmap]
rs10877185	0.83[TSI][hapmap]
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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172791	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][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]
rs11172805	0.83[TSI][hapmap]
rs11172817	0.83[TSI][hapmap]
rs11172818	0.83[TSI][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]
rs12146851	0.83[TSI][hapmap]
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]
rs2293659	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:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59257000-59270800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:59260600-59284200	Strong transcription	HUVEC	blood vessel
3	chr12:59261400-59270800	Strong transcription	Liver	Liver
4	chr12:59261400-59284200	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr12:59261600-59284200	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr12:59261800-59275000	Strong transcription	Fetal Lung	lung
7	chr12:59261800-59280800	Strong transcription	Fetal Intestine Large	intestine
8	chr12:59262600-59272400	Weak transcription	Fetal Heart	heart
9	chr12:59262600-59295000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:59263000-59276400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:59263200-59270400	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr12:59263200-59277000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:59263400-59270600	Strong transcription	A549	lung
14	chr12:59263400-59271200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:59263400-59281400	Strong transcription	NHEK	skin
16	chr12:59263600-59278800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:59264200-59274800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:59264400-59274600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:59264800-59284200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr12:59265000-59277200	Weak transcription	GM12878-XiMat	blood
21	chr12:59265200-59271000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:59265400-59275400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:59265400-59284200	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:59265600-59271200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:59265600-59276200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:59265800-59270800	Strong transcription	NHLF	lung
27	chr12:59265800-59275800	Strong transcription	Fetal Kidney	kidney
28	chr12:59266000-59282000	Strong transcription	Adipose Nuclei	Adipose
29	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
30	chr12:59266200-59270600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:59266200-59274800	Strong transcription	Colon Smooth Muscle	Colon
32	chr12:59266200-59278600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:59266200-59284000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr12:59266400-59270800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:59266400-59274800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:59266400-59274800	Strong transcription	Right Ventricle	heart
37	chr12:59266400-59274800	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:59266400-59274800	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:59266400-59275000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr12:59266400-59275400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:59266400-59275400	Strong transcription	Ovary	ovary
42	chr12:59266400-59275800	Strong transcription	Placenta	Placenta
43	chr12:59266400-59275800	Strong transcription	Left Ventricle	heart
44	chr12:59266400-59277600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:59266400-59277600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:59266400-59284000	Strong transcription	Fetal Muscle Leg	muscle
47	chr12:59266600-59270400	Strong transcription	Osteobl	bone
48	chr12:59266600-59274600	Weak transcription	Brain Germinal Matrix	brain
49	chr12:59266600-59275000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:59266600-59275400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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