Variant report

Variant	rs7162423
Chromosome Location	chr15:74052756-74052757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1038093	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs12440563	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12442096	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17187183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2123208	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28485305	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28581503	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28594180	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28655328	0.80[ASN][1000 genomes]
rs28688071	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28709470	0.80[ASN][1000 genomes]
rs3088341	0.82[ASN][1000 genomes]
rs3743098	0.83[AMR][1000 genomes]
rs4243087	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4887111	0.80[ASN][1000 genomes]
rs4887161	0.82[AFR][1000 genomes]
rs60833441	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7171779	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7172656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	nsv471252	chr15:74006691-74089793	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv569970	chr15:74016622-74059081	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7162423	COMMD4	cis	cerebellum	SCAN
rs7162423	THAP10	cis	cerebellum	SCAN
rs7162423	SCAMP2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74046000-74056200	Weak transcription	Right Atrium	heart
2	chr15:74047400-74056200	Weak transcription	Esophagus	oesophagus
3	chr15:74049800-74057000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:74051200-74056200	Weak transcription	Left Ventricle	heart
5	chr15:74052000-74056200	Weak transcription	Right Ventricle	heart
6	chr15:74052200-74053000	Enhancers	Fetal Brain Male	brain
7	chr15:74052400-74054000	Enhancers	Fetal Lung	lung
8	chr15:74052600-74059000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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