Variant report

Variant	rs978156
Chromosome Location	chr13:38277511-38277512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12429617	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61955492	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7322054	0.81[JPT][hapmap]
rs9532105	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9532106	0.82[AFR][1000 genomes]
rs9532107	0.88[JPT][hapmap]
rs9532108	0.90[GIH][hapmap]
rs9548026	1.00[ASW][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9548028	0.82[AMR][1000 genomes]
rs9548029	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548030	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548031	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9548032	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9548033	0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs978156	SMAD9	cis	cerebellum	SCAN
rs978156	POSTN	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38257400-38282000	Weak transcription	Ovary	ovary
2	chr13:38273600-38277600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr13:38274000-38277800	Enhancers	NHDF-Ad	bronchial
4	chr13:38276400-38281600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr13:38276400-38281800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr13:38276600-38282400	Weak transcription	HUVEC	blood vessel
7	chr13:38276800-38280000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:38276800-38289200	Weak transcription	NH-A	brain
9	chr13:38277000-38281400	Weak transcription	NHLF	lung
10	chr13:38277400-38288600	Weak transcription	Osteobl	bone

Quick Search:

Input of quick search could be:

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

what's new

Quick links