Variant report

Variant	rs9561374
Chromosome Location	chr13:94150012-94150013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11620291	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1445270	0.92[MEX][hapmap]
rs17234467	0.83[CHD][hapmap]
rs17267801	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs17300352	0.89[CHD][hapmap];0.90[JPT][hapmap]
rs6492664	0.94[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72640578	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72640597	0.83[EUR][1000 genomes]
rs7983734	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7997987	0.80[CHD][hapmap]
rs8000028	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9556298	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs9556299	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9556302	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9561356	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs9561361	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9561376	0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs970263	0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][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	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription 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
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv530636	chr13:93997311-94281707	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916039	chr13:94035909-94191105	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv562749	chr13:94083352-94263206	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv900920	chr13:94088707-94151937	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv1842896	chr13:94095160-94153194	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv900921	chr13:94105666-94157481	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv900922	chr13:94105666-94281492	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9561374	TGDS	cis	parietal	SCAN
rs9561374	GPR180	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94149200-94150200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr13:94149200-94150200	Enhancers	Fetal Heart	heart
3	chr13:94149400-94152200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr13:94149600-94151600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr13:94149600-94151600	Weak transcription	Fetal Stomach	stomach
6	chr13:94149600-94152000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr13:94149600-94152200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:94149600-94152200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr13:94149800-94150400	Enhancers	Fetal Brain Male	brain
10	chr13:94149800-94151800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr13:94149800-94151800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:94149800-94154400	Weak transcription	Fetal Brain Female	brain
13	chr13:94150000-94151600	Weak transcription	Fetal Lung	lung
14	chr13:94150000-94152000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr13:94150000-94157800	Weak transcription	HUES48 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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