Variant report

Variant	rs11929678
Chromosome Location	chr3:112948559-112948560
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112929883..112933461-chr3:112947415..112950895,3	MCF-7	breast:
2	chr3:112940651..112942563-chr3:112947159..112949751,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16860739	0.81[CEU][hapmap]
rs16860784	0.81[CEU][hapmap]
rs16860788	0.81[CEU][hapmap]
rs17255413	0.81[CEU][hapmap]
rs3814401	0.81[CEU][hapmap]
rs7614288	0.81[CEU][hapmap]
rs775221	0.81[CEU][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112931800-112950800	Weak transcription	Lung	lung
2	chr3:112932000-112972800	Weak transcription	Aorta	Aorta
3	chr3:112934400-112950400	Weak transcription	HSMMtube	muscle
4	chr3:112934600-112950800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112937000-112954800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:112937200-112953400	Weak transcription	Right Ventricle	heart
7	chr3:112938800-112950000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:112940600-112953400	Weak transcription	Stomach Mucosa	stomach
9	chr3:112941600-112950600	Weak transcription	Brain Anterior Caudate	brain
10	chr3:112941800-112950800	Weak transcription	Pancreas	Pancrea
11	chr3:112942200-112950000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:112942800-112950600	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:112943000-112950000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:112943000-112950600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:112943200-112949000	Weak transcription	NH-A	brain
16	chr3:112943200-112950600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:112943400-112949400	Weak transcription	NHDF-Ad	bronchial
18	chr3:112943400-112950200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:112943400-112950600	Weak transcription	Adipose Nuclei	Adipose
20	chr3:112943400-112950600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:112943600-112960600	Weak transcription	Fetal Thymus	thymus
22	chr3:112944000-112949400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:112945600-112949200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:112945800-112950400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:112946200-112951000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:112946400-112950600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:112946400-112953400	Weak transcription	Gastric	stomach
28	chr3:112946800-112948800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr3:112947000-112955600	Weak transcription	Fetal Intestine Small	intestine
30	chr3:112947400-112948600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:112947600-112950800	Weak transcription	Left Ventricle	heart
32	chr3:112947800-112949800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:112947800-112949800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:112947800-112950200	Weak transcription	HSMM	muscle
35	chr3:112947800-112950400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:112947800-112950400	Weak transcription	Ovary	ovary
37	chr3:112947800-112950600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:112948000-112948600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:112948000-112949000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:112948000-112950600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:112948000-112950600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:112948000-112950600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:112948000-112950600	Weak transcription	Brain Germinal Matrix	brain
44	chr3:112948200-112949200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:112948200-112950200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:112948200-112950400	Weak transcription	Fetal Brain Male	brain
47	chr3:112948200-112950600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:112948200-112950600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:112948200-112950600	Weak transcription	Fetal Kidney	kidney
50	chr3:112948400-112948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links