Variant report

Variant	rs1904316
Chromosome Location	chr15:49708710-49708711
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11070692	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs11634786	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12439429	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1429556	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs16962440	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28375625	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899437	0.80[YRI][hapmap]
rs34813196	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4316697	0.90[CHB][hapmap]
rs6493361	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs6493363	0.80[CHB][hapmap]
rs7164109	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8031480	0.84[JPT][hapmap];0.85[MEX][hapmap]
rs8031680	0.80[YRI][hapmap]
rs8034747	0.85[CHB][hapmap]
rs8040134	0.84[JPT][hapmap];0.85[MEX][hapmap]
rs9920722	0.93[YRI][hapmap]

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	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1904316	SECISBP2L	cis	parietal	SCAN
rs1904316	LCMT2	cis	parietal	SCAN
rs1904316	COPS2	Cis_1M	lymphoblastoid	RTeQTL
rs1904316	SPATA5L1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49703000-49709600	Weak transcription	Fetal Lung	lung
2	chr15:49707200-49709000	Enhancers	Hela-S3	cervix
3	chr15:49707400-49708800	Enhancers	NHLF	lung
4	chr15:49707600-49709400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:49708000-49708800	Enhancers	Fetal Stomach	stomach
6	chr15:49708200-49713400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:49708200-49713800	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:49708400-49708800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:49708400-49713800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:49708400-49714400	Weak transcription	HUVEC	blood vessel
11	chr15:49708600-49711200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:49708600-49714000	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