Variant report

Variant	rs12786748
Chromosome Location	chr11:85921942-85921943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10751137	1.00[YRI][hapmap]
rs10792842	1.00[YRI][hapmap]
rs10792843	0.86[ASW][hapmap];1.00[YRI][hapmap]
rs10792844	1.00[ASW][hapmap];0.91[CEU][hapmap];0.80[CHB][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap]
rs10898446	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898453	0.82[ASN][1000 genomes]
rs10898457	0.86[ASW][hapmap];0.91[YRI][hapmap]
rs11234610	0.86[ASW][hapmap]
rs11608125	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223670	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34471798	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35863758	0.85[EUR][1000 genomes]
rs7120222	1.00[YRI][hapmap]
rs7122629	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7924472	0.86[ASW][hapmap];1.00[YRI][hapmap]
rs974144	0.86[ASW][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12786748	RAB38	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85914000-85926200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:85917200-85928800	Weak transcription	Hela-S3	cervix
3	chr11:85919200-85925600	Weak transcription	Placenta	Placenta
4	chr11:85919600-85923800	Enhancers	HepG2	liver
5	chr11:85919600-85929200	Weak transcription	Right Atrium	heart
6	chr11:85920000-85925600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr11:85920400-85925800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:85920800-85923600	Enhancers	K562	blood
9	chr11:85921000-85925800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:85921000-85929000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:85921400-85922400	Weak transcription	GM12878-XiMat	blood
12	chr11:85921600-85929800	Weak transcription	Fetal Intestine Large	intestine
13	chr11:85921800-85929200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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