Variant report

Variant	rs12963759
Chromosome Location	chr18:7955787-7955788
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	chr18:7953033..7955520-chr18:7955662..7957889,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10153443	0.90[EUR][1000 genomes]
rs10163540	1.00[JPT][hapmap]
rs12326176	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326185	0.90[EUR][1000 genomes]
rs12954431	0.91[EUR][1000 genomes]
rs12956961	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12957388	0.91[EUR][1000 genomes]
rs12957993	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12959314	0.91[EUR][1000 genomes]
rs12960276	0.91[EUR][1000 genomes]
rs12966777	0.91[EUR][1000 genomes]
rs12968232	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13381485	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16952705	0.90[EUR][1000 genomes]
rs16952722	0.88[EUR][1000 genomes]
rs28434244	0.90[EUR][1000 genomes]
rs34017251	0.90[EUR][1000 genomes]
rs34046553	0.90[EUR][1000 genomes]
rs34049036	0.90[EUR][1000 genomes]
rs34296167	0.90[EUR][1000 genomes]
rs34554615	0.89[EUR][1000 genomes]
rs34580701	0.90[EUR][1000 genomes]
rs35308699	0.90[EUR][1000 genomes]
rs35434291	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35521625	0.91[EUR][1000 genomes]
rs35558945	0.91[EUR][1000 genomes]
rs35822807	0.91[EUR][1000 genomes]
rs35830277	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36093720	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7239786	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7240582	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8087770	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8087884	0.91[EUR][1000 genomes]
rs8089133	0.90[EUR][1000 genomes]
rs8092781	0.90[EUR][1000 genomes]
rs9807495	0.87[EUR][1000 genomes]
rs9952741	0.85[EUR][1000 genomes]
rs9955279	1.00[JPT][hapmap]
rs9956981	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9961079	0.90[EUR][1000 genomes]
rs9962439	1.00[JPT][hapmap]

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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7932200-7961000	Weak transcription	HepG2	liver
2	chr18:7941800-7966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr18:7946200-7958200	Weak transcription	Aorta	Aorta
4	chr18:7947200-7955800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr18:7947200-7958200	Weak transcription	Colon Smooth Muscle	Colon
6	chr18:7947200-7981400	Weak transcription	Fetal Stomach	stomach
7	chr18:7947400-7958200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr18:7947400-7958400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr18:7947400-7959200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr18:7947400-7963400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr18:7947400-7963600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:7947400-7965600	Weak transcription	Thymus	Thymus
13	chr18:7947600-7956600	Weak transcription	Brain Hippocampus Middle	brain
14	chr18:7947600-7958200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr18:7947800-7957000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr18:7947800-7957400	Weak transcription	Spleen	Spleen
17	chr18:7947800-7958400	Weak transcription	Brain Anterior Caudate	brain
18	chr18:7947800-7958400	Weak transcription	Gastric	stomach
19	chr18:7947800-7958600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr18:7947800-7967600	Weak transcription	Primary T cells from cord blood	blood
21	chr18:7948000-7956600	Weak transcription	Lung	lung
22	chr18:7948000-7957000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr18:7948000-7959600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr18:7948000-7965800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr18:7948000-7967200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr18:7948000-7975000	Weak transcription	Pancreas	Pancrea
27	chr18:7950800-7956200	Weak transcription	Fetal Intestine Small	intestine
28	chr18:7951000-7958600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr18:7951200-7958000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr18:7951200-7958200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr18:7951200-7963400	Weak transcription	Adipose Nuclei	Adipose
32	chr18:7951400-7956600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr18:7951600-7958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr18:7951600-7965800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr18:7953600-7958800	Weak transcription	Fetal Heart	heart
36	chr18:7953800-7958400	Enhancers	Hela-S3	cervix
37	chr18:7954000-7956600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr18:7954200-7957400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr18:7954200-7957400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr18:7954200-7957400	Weak transcription	GM12878-XiMat	blood
41	chr18:7954400-7956800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr18:7954400-7958200	Weak transcription	NHDF-Ad	bronchial
43	chr18:7954400-7966000	Weak transcription	Fetal Kidney	kidney
44	chr18:7955000-7956000	Enhancers	Fetal Lung	lung
45	chr18:7955000-7956000	Weak transcription	A549	lung
46	chr18:7955000-7956200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr18:7955000-7957800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr18:7955000-7958200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr18:7955000-7958200	Weak transcription	Osteobl	bone
50	chr18:7955000-7958400	Weak transcription	NH-A	brain

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