Variant report

Variant	rs4968983
Chromosome Location	chr17:66983753-66983754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10512523	0.90[CHB][hapmap]
rs11077858	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11077859	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11077860	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11077884	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11657541	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs11871766	0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs11871944	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs12325889	0.90[CHB][hapmap]
rs12939564	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12940103	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12942599	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12943969	0.80[EUR][1000 genomes]
rs1541470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16973495	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2191212	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2191213	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302294	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36096265	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4548939	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6501944	0.86[JPT][hapmap]
rs6501947	0.88[ASW][hapmap];0.91[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7207125	0.88[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7215642	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs7217543	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs7218871	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8066758	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs8068236	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8070285	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs8070357	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9303006	0.83[EUR][1000 genomes]
rs9894490	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv908700	chr17:66885526-66985992	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4968983	ABCA6	cis	parietal	SCAN
rs4968983	TACO1	cis	cerebellum	SCAN
rs4968983	ABCA9	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66965600-66986000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr17:66970800-66984000	Weak transcription	Spleen	Spleen
3	chr17:66971000-66987800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr17:66977400-66984200	Weak transcription	Gastric	stomach
5	chr17:66977400-66989400	Weak transcription	Pancreas	Pancrea
6	chr17:66977600-67001400	Weak transcription	Fetal Lung	lung
7	chr17:66977800-66984000	Weak transcription	HepG2	liver
8	chr17:66977800-66987600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr17:66977800-66991000	Weak transcription	Fetal Stomach	stomach
10	chr17:66977800-66991600	Strong transcription	Adipose Nuclei	Adipose
11	chr17:66977800-67027400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr17:66978600-66987200	Weak transcription	NHDF-Ad	bronchial
13	chr17:66978600-66988000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr17:66978600-66989400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:66979400-67005400	Weak transcription	Psoas Muscle	Psoas
16	chr17:66979600-67001200	Weak transcription	Left Ventricle	heart
17	chr17:66980400-67009400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr17:66981400-67001200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr17:66981400-67001400	Weak transcription	Fetal Muscle Leg	muscle
20	chr17:66982600-66990000	Strong transcription	Liver	Liver
21	chr17:66983400-66985000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr17:66983600-66984000	Strong transcription	Ovary	ovary
23	chr17:66983600-66988000	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links