Variant report

Variant	rs9294148
Chromosome Location	chr6:80208913-80208914
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10943650	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10943651	0.82[AMR][1000 genomes]
rs13206818	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1351959	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1354452	0.80[CHD][hapmap];0.91[MEX][hapmap]
rs1485374	0.83[JPT][hapmap]
rs2009837	0.81[AFR][1000 genomes]
rs2047896	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2655662	0.85[YRI][hapmap]
rs2655700	0.86[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2803183	0.85[ASN][1000 genomes]
rs2812689	0.82[AFR][1000 genomes]
rs3747766	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3747767	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3967183	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4055084	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4706789	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs66572100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6915859	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930436	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72624517	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7356969	0.81[AMR][1000 genomes]
rs7754849	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9341781	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9341782	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9343918	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9343919	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9343920	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9343921	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9352736	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9352737	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9352738	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9352739	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9352743	0.86[CHD][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9352744	1.00[CEU][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][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]
rs9352747	1.00[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9359379	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9359382	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9359383	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9359384	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9361537	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9361538	1.00[CEU][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9361539	0.82[AFR][1000 genomes]
rs958114	0.86[MEX][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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1030126	chr6:80113449-80209165	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv886303	chr6:80147225-80252423	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9294148	POMZP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80171200-80220000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:80171600-80226600	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:80178200-80212800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:80179800-80217200	Weak transcription	Aorta	Aorta
5	chr6:80179800-80235000	Weak transcription	HSMMtube	muscle
6	chr6:80180400-80215400	Weak transcription	Fetal Lung	lung
7	chr6:80181400-80222000	Weak transcription	Left Ventricle	heart
8	chr6:80189600-80216600	Weak transcription	Fetal Brain Female	brain
9	chr6:80189600-80225200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:80190200-80234400	Weak transcription	Fetal Intestine Large	intestine
11	chr6:80192400-80223200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:80192400-80226800	Weak transcription	Brain Anterior Caudate	brain
13	chr6:80194600-80217200	Weak transcription	Brain Germinal Matrix	brain
14	chr6:80194800-80225400	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:80195400-80235000	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:80195800-80218000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:80197400-80224200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:80197600-80220400	Weak transcription	Fetal Kidney	kidney
19	chr6:80198000-80221400	Weak transcription	HSMM	muscle
20	chr6:80198200-80217200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:80198400-80235000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:80199000-80235000	Weak transcription	Adipose Nuclei	Adipose
23	chr6:80200800-80210200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:80204800-80209000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:80207400-80214600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:80207600-80246000	Weak transcription	Ovary	ovary
27	chr6:80208600-80209000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:80208600-80209000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:80208600-80209000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:80208600-80209000	Enhancers	HepG2	liver
31	chr6:80208600-80209200	Enhancers	Liver	Liver
32	chr6:80208800-80209000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links