Variant report

Variant	rs11923198
Chromosome Location	chr3:79061664-79061665
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:79059187..79061732-chr3:79063739..79067331,3	MCF-7	breast:
2	chr3:79061171..79063415-chr3:79068475..79070021,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169855	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11127638	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12495750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13096526	0.86[EUR][1000 genomes]
rs1349023	1.00[EUR][1000 genomes]
rs1349024	1.00[EUR][1000 genomes]
rs1374883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1374885	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1374886	0.86[EUR][1000 genomes]
rs1374887	1.00[EUR][1000 genomes]
rs1374888	1.00[EUR][1000 genomes]
rs1374889	1.00[EUR][1000 genomes]
rs1900663	0.86[EUR][1000 genomes]
rs1947154	1.00[EUR][1000 genomes]
rs2871747	1.00[EUR][1000 genomes]
rs4327350	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4680946	0.86[EUR][1000 genomes]
rs61586777	0.86[EUR][1000 genomes]
rs6548603	1.00[EUR][1000 genomes]
rs6548604	0.86[EUR][1000 genomes]
rs6548605	0.86[EUR][1000 genomes]
rs6548606	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6774082	1.00[EUR][1000 genomes]
rs6788693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797152	1.00[EUR][1000 genomes]
rs6804234	0.86[EUR][1000 genomes]
rs7625043	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7646169	1.00[EUR][1000 genomes]
rs9845900	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834745	chr3:79055426-79227937	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:79040800-79062000	Weak transcription	Ovary	ovary
2	chr3:79044800-79064600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:79054400-79066600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:79054600-79061800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:79054600-79062000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:79054600-79064600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:79055600-79062000	Weak transcription	NHDF-Ad	bronchial
8	chr3:79056200-79062000	Weak transcription	Osteobl	bone
9	chr3:79057600-79061800	Enhancers	Fetal Brain Male	brain
10	chr3:79058600-79064600	Enhancers	Brain Hippocampus Middle	brain
11	chr3:79059000-79061800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:79059000-79064800	Enhancers	Brain Substantia Nigra	brain
13	chr3:79059200-79061800	Enhancers	Fetal Brain Female	brain
14	chr3:79060000-79062400	Enhancers	HepG2	liver
15	chr3:79060000-79064600	Enhancers	Fetal Lung	lung
16	chr3:79060200-79062000	Enhancers	Brain Angular Gyrus	brain
17	chr3:79060200-79062000	Active TSS	Stomach Smooth Muscle	stomach
18	chr3:79060400-79062400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:79060600-79062400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:79060600-79064600	Weak transcription	Fetal Stomach	stomach
21	chr3:79060800-79061800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:79060800-79061800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:79060800-79064400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:79061000-79062200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr3:79061000-79063600	Enhancers	Colon Smooth Muscle	Colon
26	chr3:79061000-79064600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:79061200-79061800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:79061200-79061800	Weak transcription	Aorta	Aorta
29	chr3:79061200-79062000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:79061200-79062000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr3:79061200-79062200	Enhancers	Adipose Nuclei	Adipose
32	chr3:79061200-79062600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:79061200-79063000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:79061200-79064200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:79061200-79067000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:79061400-79061800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr3:79061400-79061800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:79061400-79062000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:79061400-79062200	Enhancers	Brain Anterior Caudate	brain
40	chr3:79061400-79062600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:79061400-79062600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:79061400-79062800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:79061400-79064200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:79061400-79065800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:79061600-79061800	Enhancers	Brain Cingulate Gyrus	brain
46	chr3:79061600-79062000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:79061600-79062200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:79061600-79062600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:79061600-79062600	Enhancers	Fetal Kidney	kidney
50	chr3:79061600-79064000	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links