Variant report

Variant	rs12961753
Chromosome Location	chr18:12288748-12288749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12282293..12284100-chr18:12288664..12290381,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12965777	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12965889	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4797665	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs7505203	0.91[JPT][hapmap]
rs9635828	0.81[JPT][hapmap]
rs9807728	0.86[JPT][hapmap]
rs9989524	0.80[AMR][1000 genomes]
rs9989596	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv870342	chr18:12270808-12295798	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 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	chr18:12287000-12289000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr18:12287200-12289000	Bivalent Enhancer	Fetal Brain Male	brain
3	chr18:12287200-12289200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr18:12287200-12289400	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr18:12287400-12288800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr18:12287400-12288800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
7	chr18:12287400-12288800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
8	chr18:12287400-12289000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
9	chr18:12287400-12289000	Active TSS	Esophagus	oesophagus
10	chr18:12287400-12289400	Flanking Active TSS	NHEK	skin
11	chr18:12287600-12288800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr18:12287600-12288800	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
13	chr18:12287600-12289000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr18:12287600-12289000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
15	chr18:12287600-12289200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:12287600-12289200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr18:12287600-12289200	Enhancers	Lung	lung
18	chr18:12287600-12289200	Active TSS	Right Atrium	heart
19	chr18:12287600-12289200	Flanking Active TSS	NH-A	brain
20	chr18:12287600-12289400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr18:12287600-12289400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr18:12287800-12288800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
23	chr18:12287800-12289400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
24	chr18:12288000-12288800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr18:12288000-12288800	Bivalent/Poised TSS	Fetal Kidney	kidney
26	chr18:12288000-12288800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
27	chr18:12288000-12289400	Flanking Active TSS	K562	blood
28	chr18:12288200-12288800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:12288200-12288800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr18:12288200-12289000	Bivalent Enhancer	Liver	Liver
31	chr18:12288200-12289000	Enhancers	Gastric	stomach
32	chr18:12288200-12289200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
33	chr18:12288200-12289200	Bivalent Enhancer	Fetal Intestine Large	intestine
34	chr18:12288200-12289200	Flanking Active TSS	Left Ventricle	heart
35	chr18:12288200-12289200	Flanking Active TSS	Osteobl	bone
36	chr18:12288200-12289400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr18:12288400-12288800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr18:12288400-12288800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr18:12288400-12288800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr18:12288400-12288800	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr18:12288400-12289000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr18:12288400-12289000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
43	chr18:12288400-12289000	Bivalent Enhancer	Brain Germinal Matrix	brain
44	chr18:12288400-12289000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr18:12288400-12289000	Flanking Active TSS	Fetal Heart	heart
46	chr18:12288400-12289000	Flanking Active TSS	Hela-S3	cervix
47	chr18:12288400-12289000	Flanking Active TSS	NHDF-Ad	bronchial
48	chr18:12288400-12289200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
49	chr18:12288400-12289200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
50	chr18:12288400-12289200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links