Variant report

Variant	rs2576143
Chromosome Location	chr13:54706974-54706975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCDH8-5	chr13:54706748-54707001	ENSG00000234787
2	lnc-PCDH8-5	chr13:54706748-54707001	ENSG00000234787
3	lnc-PCDH8-5	chr13:54706748-54707001	ENSG00000234787.3
4	lnc-PCDH8-5	chr13:54706748-54707001	NONHSAT034028
5	lnc-PCDH8-5	chr13:54706748-54707006	NR_108062
6	lnc-PCDH8-5	chr13:54706748-54707006	NR_108063
7	lnc-PCDH8-5	chr13:54706748-54706997	ENSG00000234787.3
8	lnc-PCDH8-5	chr13:54706748-54706986	ENSG00000234787.3

No data

Variant related genes	Relation type
POU5F1	LncRNA region

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1335979	0.85[ASN][1000 genomes]
rs1335980	0.83[ASN][1000 genomes]
rs1537644	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1832016	0.96[AFR][1000 genomes]
rs1932503	0.85[ASN][1000 genomes]
rs2005372	0.85[ASN][1000 genomes]
rs2050534	0.85[ASN][1000 genomes]
rs2050535	0.85[ASN][1000 genomes]
rs2050536	0.85[ASN][1000 genomes]
rs2152503	0.81[ASN][1000 genomes]
rs2184678	0.85[ASN][1000 genomes]
rs2260462	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2408992	0.83[ASN][1000 genomes]
rs2408993	0.85[ASN][1000 genomes]
rs2408994	0.85[ASN][1000 genomes]
rs2408995	0.85[ASN][1000 genomes]
rs2576113	0.89[EUR][1000 genomes]
rs2576118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576144	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576148	1.00[AFR][1000 genomes]
rs2782515	0.89[EUR][1000 genomes]
rs2782517	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2782518	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2784558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs484366	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4883848	0.85[ASN][1000 genomes]
rs4883850	0.85[ASN][1000 genomes]
rs4884867	0.85[ASN][1000 genomes]
rs5002542	0.85[ASN][1000 genomes]
rs5002543	0.85[ASN][1000 genomes]
rs515604	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs518647	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs520026	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs538663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs574751	0.89[EUR][1000 genomes]
rs632059	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636911	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs664745	0.89[EUR][1000 genomes]
rs681748	0.89[EUR][1000 genomes]
rs688466	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7326186	0.83[ASN][1000 genomes]
rs7326388	0.81[ASN][1000 genomes]
rs7335475	0.85[ASN][1000 genomes]
rs795635	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs795642	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs795643	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs795652	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs795653	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs795655	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs795656	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs795658	1.00[AFR][1000 genomes]
rs797060	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7984593	0.85[ASN][1000 genomes]
rs7985320	0.85[ASN][1000 genomes]
rs7986212	0.85[ASN][1000 genomes]
rs7991755	0.85[ASN][1000 genomes]
rs7993452	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8001182	0.85[ASN][1000 genomes]
rs812128	0.89[EUR][1000 genomes]
rs878943	0.85[ASN][1000 genomes]
rs9536639	0.85[ASN][1000 genomes]
rs988526	0.85[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	esv3375545	chr13:54517432-54908108	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1049	chr13:54684354-54728981	Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2757533	chr13:54692032-54711236	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	esv2759938	chr13:54692032-54711236	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54703600-54707200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr13:54704200-54707400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr13:54704400-54707000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr13:54704400-54707000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr13:54704600-54707000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr13:54704600-54707400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr13:54704800-54707000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:54705200-54707000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:54705400-54707000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr13:54705400-54707400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr13:54706000-54707000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr13:54706200-54707000	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr13:54706400-54707000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr13:54706600-54707400	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr13:54706800-54707000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links