Variant report

Variant	rs227396
Chromosome Location	chr14:70408493-70408494
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10139615	0.84[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs10151432	0.85[EUR][1000 genomes]
rs1276120	0.88[CHD][hapmap];0.80[MEX][hapmap]
rs1314983	0.82[CHD][hapmap]
rs170567	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs190133	0.96[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227388	0.92[CEU][hapmap];0.88[CHD][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227395	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs227397	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs227398	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs927414	0.81[CHD][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	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv832824	chr14:70320639-70511401	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs227396	FAM71D	cis	cerebellum	SCAN
rs227396	SMOC1	cis	Artery Tibial	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70398400-70409400	Enhancers	Liver	Liver
2	chr14:70399600-70409600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:70403600-70411600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr14:70404800-70409400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr14:70404800-70409800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:70405200-70410800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr14:70405800-70409400	Weak transcription	Gastric	stomach
8	chr14:70406600-70408800	Enhancers	HepG2	liver
9	chr14:70407000-70409400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:70407000-70410400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr14:70407800-70411200	Enhancers	Pancreas	Pancrea
12	chr14:70408200-70409000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr14:70408200-70409000	Genic enhancers	Hela-S3	cervix
14	chr14:70408400-70408800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr14:70408400-70409600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr14:70408400-70410800	Enhancers	Fetal Intestine Large	intestine

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