Variant report

Variant	rs10414731
Chromosome Location	chr19:35970479-35970480
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10410228	0.92[AMR][1000 genomes]
rs10421540	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10425364	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10426552	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11880364	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs11880530	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17638216	1.00[ASW][hapmap];0.82[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17705401	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17705416	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17705450	0.87[AMR][1000 genomes]
rs28561458	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59551721	0.85[ASN][1000 genomes]
rs62111717	0.90[AMR][1000 genomes]
rs6510489	1.00[ASN][1000 genomes]
rs7976	1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]
rs8103133	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8106676	0.85[ASN][1000 genomes]
rs8107732	0.85[ASN][1000 genomes]
rs9973222	0.82[GIH][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
5	nsv833811	chr19:35850257-36029535	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1057692	chr19:35949892-35984103	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv543994	chr19:35949892-35984103	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10414731	LGALS16	cis	parietal	SCAN
rs10414731	PSG1	cis	parietal	SCAN
rs10414731	ZNF428	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35961800-35972400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:35969400-35970600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:35969800-35970600	Enhancers	Fetal Brain Male	brain
4	chr19:35969800-35971600	Weak transcription	HepG2	liver
5	chr19:35970000-35971000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:35970400-35970600	Active TSS	Brain Germinal Matrix	brain

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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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