Variant report

Variant	rs11739327
Chromosome Location	chr5:166717990-166717991
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10043619	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10462891	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10475839	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13355217	1.00[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4075224	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4349736	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56857681	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59094139	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61241624	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6865179	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7341056	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7730469	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7731005	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869374	chr5:166488702-166817411	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1032183	chr5:166612188-166732287	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	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
rs11739327	LOC257358	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:166707800-166718600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:166709400-166719800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:166714200-166719800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:166714800-166721600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:166715000-166719200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:166715000-166720800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:166715000-166722200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:166715000-166722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:166716000-166718400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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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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