Variant report

Variant	rs7439493
Chromosome Location	chr4:110656730-110656731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10004377	0.89[ASW][hapmap];0.88[CEU][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs11728699	1.00[ASW][hapmap];0.89[CEU][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13117504	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1541373	0.89[ASW][hapmap];0.80[CEU][hapmap]
rs2301717	0.89[ASW][hapmap];0.80[CEU][hapmap]
rs3181187	0.80[CEU][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap]
rs4698780	0.92[LWK][hapmap]
rs4698782	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5030535	0.80[CEU][hapmap];0.83[YRI][hapmap]
rs5030539	0.80[CEU][hapmap]
rs6533444	0.88[LWK][hapmap]
rs6533451	0.89[ASW][hapmap];0.80[CEU][hapmap]
rs6831917	0.89[ASW][hapmap];0.80[CEU][hapmap]
rs6854876	0.85[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72674868	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7674356	0.89[ASW][hapmap];0.80[CEU][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs7694620	0.89[ASW][hapmap];0.80[CEU][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs9992400	0.80[CEU][hapmap];0.84[YRI][hapmap]
rs9995011	1.00[ASW][hapmap];0.89[CEU][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

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	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv4463	chr4:110647731-110693125	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7439493	CASP6	cis	cerebellum	SCAN
rs7439493	LARP7	cis	parietal	SCAN
rs7439493	CASP6	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110651600-110662000	Weak transcription	HepG2	liver
2	chr4:110651800-110657000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:110651800-110657800	Weak transcription	Small Intestine	intestine
4	chr4:110651800-110669400	Weak transcription	Spleen	Spleen
5	chr4:110652000-110662400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:110652000-110682800	Weak transcription	Left Ventricle	heart
7	chr4:110652000-110686000	Weak transcription	Ovary	ovary
8	chr4:110652200-110656800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:110652200-110657600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:110652400-110656800	Weak transcription	Pancreas	Pancrea
11	chr4:110654600-110656800	Enhancers	K562	blood
12	chr4:110654800-110659200	Enhancers	Fetal Intestine Large	intestine
13	chr4:110655000-110658400	Enhancers	Fetal Intestine Small	intestine
14	chr4:110656400-110658400	Enhancers	Liver	Liver
15	chr4:110656600-110658000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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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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