Variant report

Variant	rs857938
Chromosome Location	chr1:158655458-158655459
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs16841001	0.87[YRI][hapmap]
rs2427804	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2518493	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs28568406	0.85[EUR][1000 genomes]
rs399848	0.84[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs703118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs703127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703134	0.96[EUR][1000 genomes]
rs703143	0.84[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs703144	0.89[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs703146	0.81[AFR][1000 genomes]
rs751258	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs857691	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs857703	0.88[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs857925	0.84[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs857940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861409	0.88[JPT][hapmap]
rs863327	0.80[CHD][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap]
rs864149	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3491788	chr1:158537183-158725907	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3491789	chr1:158537242-158725858	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv872481	chr1:158625789-158712510	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv872482	chr1:158635852-158698532	Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv872483	chr1:158635852-158712510	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs857938	EFNA3	cis	parietal	SCAN
rs857938	SCAMP3	cis	parietal	SCAN
rs857938	NCSTN	cis	parietal	SCAN
rs857938	KIRREL	cis	cerebellum	SCAN
rs857938	ROBLD3	cis	parietal	SCAN
rs857938	S100A7A	cis	cerebellum	SCAN
rs857938	IQGAP3	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158652200-158656200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr1:158655200-158657000	Active TSS	K562	blood

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