Variant report

Variant	rs4340305
Chromosome Location	chr15:39001315-39001316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:38999913..39002217-chr15:39871957..39874433,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2624274	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2643218	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60901913	0.96[ASN][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	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	36 gene(s)	inside rSNPs	diseases
2	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4340305	LPCAT4	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38995400-39002200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:38997400-39002000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr15:38999400-39001400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr15:38999400-39001800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr15:38999600-39001600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr15:38999600-39006000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:38999800-39001800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr15:39000000-39001400	Enhancers	HUVEC	blood vessel
9	chr15:39000000-39001600	Enhancers	Fetal Kidney	kidney
10	chr15:39000000-39002800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:39000000-39003200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:39000200-39001800	Enhancers	Fetal Intestine Small	intestine
13	chr15:39000200-39001800	Enhancers	Osteobl	bone
14	chr15:39000400-39001400	Enhancers	Rectal Smooth Muscle	rectum
15	chr15:39000400-39001600	Enhancers	HSMMtube	muscle
16	chr15:39000400-39001800	Enhancers	NH-A	brain
17	chr15:39000400-39002000	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr15:39000400-39002200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr15:39000600-39001600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:39000600-39001800	Enhancers	NHLF	lung
21	chr15:39000600-39005800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:39000800-39001400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:39001000-39001400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr15:39001000-39001600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:39001000-39001600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:39001200-39001600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr15:39001200-39005600	Weak transcription	HSMM	muscle
28	chr15:39001200-39005800	Weak transcription	NHDF-Ad	bronchial
29	chr15:39001200-39006600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:39001200-39006600	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:39001200-39006600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:39001200-39006800	Weak transcription	Fetal Brain Male	brain

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