Variant report

Variant	rs12970964
Chromosome Location	chr18:12408230-12408231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12375996..12378292-chr18:12406153..12409059,2	MCF-7	breast:
2	chr18:12406749..12409861-chr18:12418820..12421803,8	MCF-7	breast:
3	chr18:12374593..12378692-chr18:12406477..12410976,5	K562	blood:
4	chr18:12404079..12409500-chr18:12655702..12659746,9	K562	blood:
5	chr18:12406252..12409116-chr18:12699672..12701773,2	MCF-7	breast:
6	chr18:12395095..12397958-chr18:12408142..12409691,2	MCF-7	breast:
7	chr11:71823348..71823895-chr18:12407725..12408414,2	Hela-S3	cervix:
8	chr18:12407594..12413164-chr18:12414407..12422412,12	MCF-7	breast:
9	chr18:12407919..12409639-chr18:12432525..12434212,2	MCF-7	breast:
10	chr18:12375261..12378325-chr18:12405563..12409497,4	MCF-7	breast:
11	chr18:12395807..12401661-chr18:12404688..12409428,6	K562	blood:
12	chr18:12406559..12410304-chr18:12656888..12659730,4	MCF-7	breast:
13	chr18:12407968..12410146-chr3:156930881..156932746,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128789	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000251937	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000141391	Chromatin interaction
ENSG00000267108	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000110200	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12956344	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35866328	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36078796	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7243316	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72875353	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking 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	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1060728	chr18:12364077-12410409	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 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	chr18:12406400-12408400	Enhancers	Fetal Brain Male	brain
2	chr18:12406400-12408600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr18:12406800-12408600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:12407000-12408400	Active TSS	Rectal Smooth Muscle	rectum
5	chr18:12407000-12408600	Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr18:12407000-12408600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:12407000-12408600	Active TSS	Brain Hippocampus Middle	brain
8	chr18:12407000-12409000	Active TSS	Stomach Smooth Muscle	stomach
9	chr18:12407000-12409200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr18:12407200-12408600	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr18:12407200-12408600	Active TSS	Brain Angular Gyrus	brain
12	chr18:12407200-12408600	Active TSS	Ovary	ovary
13	chr18:12407200-12408600	Active TSS	Hela-S3	cervix
14	chr18:12407200-12408600	Active TSS	Osteobl	bone
15	chr18:12407200-12409000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr18:12407200-12410000	Active TSS	Fetal Brain Female	brain
17	chr18:12407400-12408400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr18:12407400-12408400	Active TSS	Muscle Satellite Cultured Cells	--
19	chr18:12407400-12408400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr18:12407400-12408400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr18:12407400-12408400	Active TSS	Adipose Nuclei	Adipose
22	chr18:12407400-12408600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:12407400-12408600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr18:12407400-12408600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr18:12407400-12408600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr18:12407400-12408600	Active TSS	Brain Anterior Caudate	brain
27	chr18:12407400-12408600	Active TSS	Brain Cingulate Gyrus	brain
28	chr18:12407400-12408600	Active TSS	Colon Smooth Muscle	Colon
29	chr18:12407400-12408600	Active TSS	Fetal Kidney	kidney
30	chr18:12407400-12408600	Active TSS	Right Ventricle	heart
31	chr18:12407400-12408800	Active TSS	Brain Germinal Matrix	brain
32	chr18:12407400-12408800	Active TSS	Brain Substantia Nigra	brain
33	chr18:12407400-12409000	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr18:12407400-12409000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr18:12407400-12409000	Active TSS	Duodenum Mucosa	Duodenum
36	chr18:12407600-12408400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr18:12407600-12408400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr18:12407600-12408600	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr18:12407600-12408600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr18:12407600-12408600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr18:12407600-12408600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr18:12407600-12408600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr18:12407600-12408600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr18:12407600-12408600	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr18:12407600-12408600	Active TSS	Gastric	stomach
46	chr18:12407600-12408600	Active TSS	Left Ventricle	heart
47	chr18:12407600-12408600	Active TSS	GM12878-XiMat	blood
48	chr18:12407600-12408800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr18:12407600-12408800	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr18:12407600-12408800	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links