Variant report

Variant	rs11172783
Chromosome Location	chr12:59260139-59260140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59259480..59262416-chr12:59311926..59314083,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139263	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10877178	1.00[CHB][hapmap]
rs10877180	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10877182	1.00[CHB][hapmap];1.00[JPT][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];0.81[ASN][1000 genomes]
rs11172773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172791	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172795	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11172797	1.00[CHB][hapmap]
rs1148531	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11514001	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][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	1.00[CHB][hapmap]
rs2279718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74099636	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3440532	chr12:59244734-59266539	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59243200-59263600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:59251000-59266400	Weak transcription	Esophagus	oesophagus
3	chr12:59251200-59261800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:59251400-59261400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:59251800-59263400	Weak transcription	NHEK	skin
6	chr12:59253000-59270200	Weak transcription	Fetal Brain Male	brain
7	chr12:59253400-59265400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:59254400-59261600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:59254600-59262000	Weak transcription	Osteobl	bone
10	chr12:59254600-59268600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:59254800-59262200	Weak transcription	Stomach Mucosa	stomach
12	chr12:59254800-59266400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:59254800-59267000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr12:59255000-59265400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:59255000-59267400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:59255200-59263400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:59255400-59267000	Weak transcription	Pancreas	Pancrea
18	chr12:59256000-59261400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:59256200-59261800	Weak transcription	NHLF	lung
20	chr12:59256200-59266400	Weak transcription	Left Ventricle	heart
21	chr12:59256400-59261800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:59256400-59262200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:59256400-59262400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:59256600-59266400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:59256800-59263600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:59257000-59270800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:59257400-59264600	Strong transcription	NHDF-Ad	bronchial
28	chr12:59257600-59263400	Weak transcription	A549	lung
29	chr12:59257600-59266600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:59257800-59262600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:59257800-59265400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:59258000-59266400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:59258000-59266800	Weak transcription	Psoas Muscle	Psoas
34	chr12:59258000-59267000	Weak transcription	Gastric	stomach
35	chr12:59258000-59267200	Weak transcription	Aorta	Aorta
36	chr12:59258200-59261400	Weak transcription	NH-A	brain
37	chr12:59258400-59260600	Weak transcription	HUVEC	blood vessel
38	chr12:59258400-59261800	Weak transcription	Fetal Lung	lung
39	chr12:59258600-59261400	Weak transcription	Fetal Kidney	kidney
40	chr12:59258600-59261600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:59258600-59267000	Weak transcription	Lung	lung
42	chr12:59258800-59261400	Weak transcription	Liver	Liver
43	chr12:59258800-59261400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:59258800-59262200	Weak transcription	Ovary	ovary
45	chr12:59258800-59263200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:59258800-59265400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:59258800-59266400	Weak transcription	Colonic Mucosa	Colon
48	chr12:59258800-59266400	Weak transcription	Right Ventricle	heart
49	chr12:59258800-59266600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:59258800-59266800	Weak transcription	Brain Hippocampus Middle	brain

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