Variant report

Variant	rs4296403
Chromosome Location	chr2:11838141-11838142
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	chr2:11837517..11840283-chr2:11849750..11852700,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10084363	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10167619	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10168372	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10179409	0.84[EUR][1000 genomes]
rs10206665	0.84[JPT][hapmap]
rs10209047	0.81[JPT][hapmap]
rs11683832	0.92[ASN][1000 genomes]
rs11886222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4564747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622687	0.84[EUR][1000 genomes]
rs57055669	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59844400	0.87[EUR][1000 genomes]
rs6432232	0.81[AMR][1000 genomes]
rs6432233	0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs6708244	0.82[CHB][hapmap]
rs67979481	0.87[ASN][1000 genomes]
rs7574891	0.87[EUR][1000 genomes]
rs9287737	0.86[EUR][1000 genomes]
rs9287738	0.84[EUR][1000 genomes]

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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv469449	chr2:11808654-11854012	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv580972	chr2:11808654-11854012	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4296403	LPIN1	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11829200-11838400	Weak transcription	Fetal Lung	lung
2	chr2:11829400-11841800	Weak transcription	Primary B cells from cord blood	blood
3	chr2:11833600-11841800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:11835400-11839200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:11836000-11839000	Enhancers	Primary hematopoietic stem cells	blood
6	chr2:11836400-11839000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:11836600-11838200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:11836600-11838200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:11836600-11838200	Enhancers	Ovary	ovary
10	chr2:11836600-11838200	Enhancers	HMEC	breast
11	chr2:11836600-11838400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:11836600-11838400	Bivalent Enhancer	Fetal Stomach	stomach
13	chr2:11836600-11838400	Enhancers	Fetal Thymus	thymus
14	chr2:11836600-11838600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:11836600-11838600	Enhancers	A549	lung
16	chr2:11836600-11838800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:11836600-11839000	Enhancers	Esophagus	oesophagus
18	chr2:11836600-11839000	Enhancers	NHDF-Ad	bronchial
19	chr2:11836600-11839000	Enhancers	NHEK	skin
20	chr2:11836600-11839000	Enhancers	NHLF	lung
21	chr2:11836600-11839200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:11836600-11839200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:11836800-11838400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:11836800-11838400	Enhancers	Left Ventricle	heart
25	chr2:11836800-11838400	Enhancers	Lung	lung
26	chr2:11836800-11838400	Enhancers	Osteobl	bone
27	chr2:11836800-11839000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr2:11836800-11839000	Enhancers	Adipose Nuclei	Adipose
29	chr2:11836800-11839000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr2:11836800-11839000	Enhancers	Right Ventricle	heart
31	chr2:11836800-11839200	Enhancers	Brain Substantia Nigra	brain
32	chr2:11836800-11839200	Enhancers	Colon Smooth Muscle	Colon
33	chr2:11836800-11839200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr2:11836800-11839800	Enhancers	Fetal Muscle Leg	muscle
35	chr2:11836800-11843200	Enhancers	Placenta	Placenta
36	chr2:11837000-11838200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:11837000-11838800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr2:11837000-11839200	Enhancers	Brain Angular Gyrus	brain
39	chr2:11837000-11839200	Enhancers	Fetal Heart	heart
40	chr2:11837200-11838600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:11837200-11839000	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr2:11837400-11838200	Weak transcription	Brain Anterior Caudate	brain
43	chr2:11837400-11838200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr2:11837400-11838400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:11837400-11839200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:11837400-11840800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:11837600-11838600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:11837600-11839000	Weak transcription	Psoas Muscle	Psoas
49	chr2:11837600-11839200	Enhancers	Brain Hippocampus Middle	brain
50	chr2:11837600-11839200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links