Variant report

Variant	rs9289034
Chromosome Location	chr3:115720093-115720094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:115718424..115720399-chr3:115727607..115730544,2	K562	blood:
2	chr3:115714015..115716158-chr3:115718030..115720877,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11918028	0.80[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12485818	0.89[CHD][hapmap]
rs12495426	0.89[CHD][hapmap]
rs13086615	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1920382	0.89[CHD][hapmap]
rs1920383	0.89[CHD][hapmap];0.86[JPT][hapmap]
rs1920384	0.80[ASW][hapmap];0.89[CHD][hapmap]
rs1920388	0.86[ASW][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs35764849	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4131452	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4131453	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4240163	0.85[ASN][1000 genomes]
rs4240164	0.81[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4240165	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4240166	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs4286426	0.92[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4315682	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4378955	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4398428	0.88[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4399891	0.92[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4426677	0.96[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4518124	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4599302	0.86[ASN][1000 genomes]
rs4611819	0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4831218	0.92[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4831219	0.92[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4831220	0.85[ASN][1000 genomes]
rs4831221	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4831222	0.96[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4831223	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs6438296	0.81[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6776244	0.89[CHD][hapmap];0.81[TSI][hapmap]
rs6777196	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6787687	0.86[ASW][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6787872	0.86[ASW][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs6789600	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6790290	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6795318	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6804278	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6807809	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7610371	0.89[CHD][hapmap]
rs7625191	0.81[ASW][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs7632252	0.94[ASN][1000 genomes]
rs9289033	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289040	0.86[CHD][hapmap]
rs9813153	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9815418	0.83[ASN][1000 genomes]
rs9833319	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9840787	0.92[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9848298	0.96[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9850406	0.86[ASN][1000 genomes]
rs9863087	0.81[ASW][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9869887	0.86[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs9872913	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs9873260	0.84[ASN][1000 genomes]
rs9878286	0.86[CHD][hapmap]

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	nsv931948	chr3:114884574-115802562	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2760762	chr3:115476222-115807650	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv829685	chr3:115643521-115812913	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9289034	POPDC2	cis	cerebellum	SCAN
rs9289034	B4GALT4	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115717400-115720400	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr3:115718000-115720200	Enhancers	HSMMtube	muscle
3	chr3:115718000-115721400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:115718000-115721400	Enhancers	HSMM	muscle
5	chr3:115718200-115720600	Enhancers	NHLF	lung
6	chr3:115718200-115721800	Enhancers	Osteobl	bone
7	chr3:115718400-115721200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:115718400-115721400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:115718400-115721600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:115718400-115721800	Enhancers	HMEC	breast
11	chr3:115718400-115722800	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr3:115718600-115721600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:115718600-115721600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:115718800-115721400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:115719000-115721000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:115719000-115721000	Weak transcription	Brain Substantia Nigra	brain
17	chr3:115719200-115721000	Enhancers	NH-A	brain
18	chr3:115719400-115720400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:115719400-115720400	Enhancers	Colon Smooth Muscle	Colon
20	chr3:115719400-115720600	Enhancers	Fetal Brain Male	brain
21	chr3:115719400-115723800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:115719400-115724200	Weak transcription	Brain Anterior Caudate	brain
23	chr3:115719600-115720400	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:115719600-115721000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:115719600-115721000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:115719600-115721600	Enhancers	NHDF-Ad	bronchial
27	chr3:115719600-115722400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:115719600-115742600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:115719800-115720200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:115719800-115721600	Enhancers	NHEK	skin
31	chr3:115719800-115721800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:115719800-115732000	Weak transcription	Hela-S3	cervix
33	chr3:115720000-115720200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr3:115720000-115720400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:115720000-115721200	Enhancers	A549	lung
36	chr3:115720000-115721400	Weak transcription	GM12878-XiMat	blood
37	chr3:115720000-115721600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:115720000-115723800	Weak transcription	K562	blood
39	chr3:115720000-115724000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:115720000-115726800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links