Variant report

Variant	rs4886979
Chromosome Location	chr15:78230906-78230907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10444863	1.00[YRI][hapmap]
rs11072698	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs11072702	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs11635732	0.88[ASN][1000 genomes]
rs11638292	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11638419	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs12593545	1.00[YRI][hapmap]
rs12908305	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs12910083	1.00[LWK][hapmap]
rs16969422	1.00[YRI][hapmap]
rs34481949	0.88[ASN][1000 genomes]
rs4479193	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs4514642	0.81[CHB][hapmap]
rs4886543	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap]
rs4886547	0.81[AMR][1000 genomes]
rs4886992	1.00[YRI][hapmap]
rs72732509	0.81[EUR][1000 genomes]
rs72732511	0.83[EUR][1000 genomes]
rs872926	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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 target site	80 gene(s)	inside rSNPs	diseases
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv904426	chr15:78090630-78264164	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904427	chr15:78129964-78251431	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv976954	chr15:78153346-78255825	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv904428	chr15:78156238-78230906	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv904429	chr15:78160362-78251431	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886979	IDH3A	cis	cerebellum	SCAN
rs4886979	PSMA4	cis	cerebellum	SCAN
rs4886979	SH2D7	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78225400-78231400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:78226800-78236200	Weak transcription	Spleen	Spleen
3	chr15:78229600-78231000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:78229600-78231400	Weak transcription	HepG2	liver
5	chr15:78230600-78231800	Enhancers	Fetal Lung	lung

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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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