Variant report

Variant	rs60293665
Chromosome Location	chr13:54705065-54705066
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:54704934-54705297	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr13:54704931-54705179	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr13:54704901-54705188	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr13:54704934-54705304	H1-hESC	embryonic stem cell:	n/a	n/a
5	SRF	chr13:54705059-54705171	GM12878	blood:	n/a	n/a

No data

No data

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCDH8-5	chr13:54705009-54705206	ENSG00000234787
2	lnc-PCDH8-5	chr13:54705009-54705206	ENSG00000234787
3	lnc-PCDH8-5	chr13:54705009-54705206	NONHSAT034028
4	lnc-PCDH8-5	chr13:54705009-54705206	NR_108062
5	lnc-PCDH8-5	chr13:54705009-54705206	NR_108063
6	lnc-PCDH8-5	chr13:54705009-54705206	ENSG00000234787.3
7	lnc-PCDH8-5	chr13:54705009-54705206	ENSG00000234787.3

No data

No data

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2576147	0.87[ASN][1000 genomes]
rs57011432	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57797655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57859453	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60446276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316704	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs933101	0.87[ASN][1000 genomes]
rs9591567	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9596918	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596919	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];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	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	chr13:54689000-54706000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:54691800-54706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:54701000-54705200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:54702800-54706600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
5	chr13:54703600-54707200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr13:54704200-54705400	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
7	chr13:54704200-54707400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr13:54704400-54707000	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr13:54704400-54707000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr13:54704600-54707000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr13:54704600-54707400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr13:54704800-54706200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:54704800-54707000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:54705000-54705200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr13:54705000-54705600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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