Variant report

Variant	rs58084121
Chromosome Location	chr15:39712893-39712894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FSIP1-5	chr15:39712745-39712910	ENSG00000259345.1

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11070202	0.86[EUR][1000 genomes]
rs12148895	0.82[AMR][1000 genomes]
rs12906753	0.80[EUR][1000 genomes]
rs12907239	0.82[EUR][1000 genomes]
rs4244569	0.82[EUR][1000 genomes]
rs4306475	0.82[EUR][1000 genomes]
rs4344715	0.86[EUR][1000 genomes]
rs4405525	0.86[EUR][1000 genomes]
rs4522393	0.82[EUR][1000 genomes]
rs4923826	0.88[EUR][1000 genomes]
rs4924354	0.82[EUR][1000 genomes]
rs55638424	0.83[EUR][1000 genomes]
rs57817952	0.87[EUR][1000 genomes]
rs59238363	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6492889	0.82[EUR][1000 genomes]
rs8026812	0.82[EUR][1000 genomes]
rs8029673	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58084121	RP11-624L4.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39704200-39718800	Weak transcription	Thymus	Thymus
2	chr15:39712000-39713000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr15:39712000-39713200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr15:39712200-39713000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:39712400-39713000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr15:39712400-39713000	Enhancers	Primary T cells from cord blood	blood
7	chr15:39712400-39713000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr15:39712400-39713200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:39712600-39713000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:39712600-39713000	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr15:39712600-39713000	Active TSS	K562	blood
12	chr15:39712600-39713200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr15:39712600-39713200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr15:39712600-39713200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:39712600-39713200	Active TSS	Duodenum Mucosa	Duodenum
16	chr15:39712600-39713400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:39712600-39719000	Weak transcription	Right Ventricle	heart
18	chr15:39712600-39724200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:39712800-39713000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr15:39712800-39713000	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr15:39712800-39713000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:39712800-39713200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:39712800-39713200	Active TSS	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links