Variant report

Variant	rs58391484
Chromosome Location	chr13:95358418-95358419
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr13:95357175-95358521	H1-hESC	embryonic stem cell:	n/a	chr13:95358229-95358238
2	E2F6	chr13:95356949-95358691	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95357906..95359959-chr13:95361552..95364059,2	MCF-7	breast:
2	chr13:95325863..95327596-chr13:95357586..95359779,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SOX21-1	chr13:95358391-95358541	ENSG00000248922
2	lnc-SOX21-1	chr13:95358391-95359564	XLOC_010695
3	lnc-SOX21-1	chr13:95358391-95358541	NONHSAT034735
4	lnc-SOX21-1	chr13:95358391-95358684	NONHSAT034737

No data

Variant related genes	Relation type
LINC00391	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11840596	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840695	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841629	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841977	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841993	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11843073	1.00[ASN][1000 genomes]
rs11843396	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16950001	1.00[ASN][1000 genomes]
rs16950006	1.00[ASN][1000 genomes]
rs16950115	1.00[ASN][1000 genomes]
rs28376374	1.00[ASN][1000 genomes]
rs41389945	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55691901	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55784615	1.00[ASN][1000 genomes]
rs55813732	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55944290	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56390739	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57648108	1.00[ASN][1000 genomes]
rs61185933	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61965578	1.00[ASN][1000 genomes]
rs6492745	1.00[ASN][1000 genomes]
rs72638373	1.00[ASN][1000 genomes]
rs72638377	1.00[ASN][1000 genomes]
rs72638380	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72638383	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72638386	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72638401	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7317507	1.00[ASN][1000 genomes]
rs9301994	1.00[ASN][1000 genomes]
rs9584248	1.00[ASN][1000 genomes]
rs9590059	1.00[ASN][1000 genomes]
rs9590075	1.00[ASN][1000 genomes]
rs9590076	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv1813549	chr13:95333331-95377127	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1824604	chr13:95357807-95365771	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95354600-95358600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr13:95355800-95359600	Weak transcription	Pancreas	Pancrea
3	chr13:95356400-95358600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:95357200-95359600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
5	chr13:95357600-95360800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:95357800-95359600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
7	chr13:95358000-95358600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:95358000-95358600	Bivalent Enhancer	Brain Anterior Caudate	brain
9	chr13:95358200-95358600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr13:95358200-95358600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr13:95358400-95358600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr13:95358400-95358600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
13	chr13:95358400-95358600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
14	chr13:95358400-95358600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
15	chr13:95358400-95358600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:95358400-95358800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:95358400-95358800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr13:95358400-95358800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr13:95358400-95358800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
20	chr13:95358400-95358800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:95358400-95361600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
22	chr13:95358400-95361600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links