Variant report

Variant	rs153053
Chromosome Location	chr16:69446319-69446320
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10048086	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs11075720	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153058	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246132	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs246138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs246140	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs246142	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs246143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs246144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs246145	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs246148	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3743670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4783708	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6499227	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7185800	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7206737	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs728546	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs8064195	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs862349	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	nsv1064808	chr16:69271190-69552951	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv542940	chr16:69271190-69552951	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs153053	LCAT	cis	parietal	SCAN
rs153053	ZNF23	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69438800-69447000	Weak transcription	Pancreas	Pancrea
2	chr16:69439000-69450600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr16:69439400-69451400	Weak transcription	Fetal Muscle Leg	muscle
4	chr16:69440200-69451600	Weak transcription	Adipose Nuclei	Adipose
5	chr16:69441200-69449600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr16:69442600-69451400	Weak transcription	Spleen	Spleen
7	chr16:69442600-69451600	Weak transcription	Fetal Intestine Small	intestine
8	chr16:69443000-69451400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr16:69443400-69448800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr16:69443400-69449000	Weak transcription	Stomach Mucosa	stomach
11	chr16:69444200-69451200	Enhancers	HepG2	liver
12	chr16:69444400-69446600	Enhancers	Fetal Thymus	thymus
13	chr16:69444600-69451400	Weak transcription	Brain Anterior Caudate	brain
14	chr16:69444800-69446400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr16:69444800-69447400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr16:69444800-69447400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr16:69444800-69447800	Enhancers	A549	lung
18	chr16:69444800-69451400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr16:69445200-69447000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr16:69445400-69446600	Enhancers	NH-A	brain
21	chr16:69445400-69450600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr16:69445400-69451200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr16:69445800-69446400	Enhancers	Osteobl	bone
24	chr16:69445800-69451400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr16:69445800-69451600	Weak transcription	Placenta	Placenta
26	chr16:69446000-69446800	Weak transcription	K562	blood
27	chr16:69446200-69446600	Enhancers	Esophagus	oesophagus
28	chr16:69446200-69447600	Enhancers	Hela-S3	cervix

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