Variant report

Variant	rs261114
Chromosome Location	chr5:101552955-101552956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11957520	0.86[LWK][hapmap];0.83[YRI][hapmap]
rs261112	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs379079	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs381316	0.82[EUR][1000 genomes]
rs382486	0.82[EUR][1000 genomes]
rs391828	0.82[EUR][1000 genomes]
rs392924	0.82[EUR][1000 genomes]
rs411954	0.82[EUR][1000 genomes]
rs433467	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs435060	0.81[EUR][1000 genomes]
rs438267	0.84[AMR][1000 genomes]
rs441067	0.81[EUR][1000 genomes]
rs6887058	0.86[LWK][hapmap]
rs72777909	0.83[AFR][1000 genomes]
rs7735136	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022551	chr5:101366177-101649643	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv882505	chr5:101397849-101652251	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1028787	chr5:101432086-101718569	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1030146	chr5:101481484-101575463	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv817537	chr5:101489151-101992104	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1031513	chr5:101531317-101564047	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1019248	chr5:101531317-101564111	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2760945	chr5:101531329-101564111	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1016176	chr5:101534391-102333606	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv537831	chr5:101534391-102333606	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv520047	chr5:101541784-101566107	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs261114	PAM	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:101551800-101553000	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr5:101551800-101553200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr5:101551800-101553200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr5:101551800-101553400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:101551800-101555000	Enhancers	HepG2	liver
6	chr5:101552000-101553200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:101552200-101553200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:101552400-101553400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:101552600-101553200	Enhancers	Liver	Liver

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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