Variant report

Variant	rs7141840
Chromosome Location	chr14:39703324-39703325
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	chr14:39571162..39573957-chr14:39700069..39703541,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100934	Chromatin interaction
ENSG00000258651	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10137623	0.88[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10142479	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10144445	0.93[ASN][1000 genomes]
rs11622951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12433610	0.80[CHD][hapmap];0.89[JPT][hapmap]
rs17092065	0.92[ASN][1000 genomes]
rs1980609	0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs1998193	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2025027	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2025028	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs28502509	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs4902459	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4902460	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6571911	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6571912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6571921	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs7147869	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7153074	0.85[JPT][hapmap]
rs7153523	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs8006319	0.91[ASN][1000 genomes]
rs9322996	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs9743804	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv84871	chr14:39698400-39707997	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7141840	LRFN5	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39674000-39705400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:39702000-39703400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr14:39702000-39703400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr14:39702000-39703600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr14:39702000-39703600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr14:39702000-39704000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr14:39702200-39703400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr14:39702200-39703400	Enhancers	HSMMtube	muscle
9	chr14:39702200-39703600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr14:39702200-39703600	Flanking Active TSS	A549	lung
11	chr14:39702400-39703400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:39702400-39703400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr14:39702400-39704000	Enhancers	HMEC	breast
14	chr14:39702600-39703400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:39702600-39703600	Enhancers	Osteobl	bone
16	chr14:39702600-39704000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr14:39702800-39705200	Active TSS	Liver	Liver
18	chr14:39703000-39703400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr14:39703000-39703400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr14:39703000-39703400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr14:39703000-39703400	Bivalent/Poised TSS	HepG2	liver
22	chr14:39703000-39703400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr14:39703000-39703600	Active TSS	Fetal Kidney	kidney
24	chr14:39703000-39704000	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr14:39703000-39704400	Active TSS	Duodenum Mucosa	Duodenum
26	chr14:39703000-39705400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr14:39703000-39706400	Active TSS	Fetal Intestine Large	intestine
28	chr14:39703000-39706400	Active TSS	Fetal Intestine Small	intestine
29	chr14:39703200-39703400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr14:39703200-39703400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr14:39703200-39703400	Enhancers	NHEK	skin
32	chr14:39703200-39703600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr14:39703200-39703600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr14:39703200-39703600	Active TSS	Fetal Stomach	stomach
35	chr14:39703200-39703600	Active TSS	Pancreas	Pancrea
36	chr14:39703200-39703600	Active TSS	Rectal Smooth Muscle	rectum
37	chr14:39703200-39703600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr14:39703200-39703600	Active TSS	Stomach Mucosa	stomach
39	chr14:39703200-39703800	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links