Variant report

Variant	rs2812297
Chromosome Location	chr9:108207197-108207198
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	chr9:108206685..108208191-chr9:108209872..108211724,2	K562	blood:
2	chr9:108196491..108199020-chr9:108207109..108209245,2	K562	blood:

Variant related genes	Relation type
ENSG00000106701	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10761100	0.80[ASN][1000 genomes]
rs10816284	0.93[YRI][hapmap]
rs10820810	0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs10820812	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10820813	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs1327354	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1360089	0.81[ASN][1000 genomes]
rs1806898	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1815383	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1960023	0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2518112	0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.80[ASN][1000 genomes]
rs2518114	0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2518116	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs2518120	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2518123	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2768279	0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2768283	0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2768290	0.84[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs2768291	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2771038	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2771041	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2771042	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2812303	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2812307	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2812308	0.82[ASN][1000 genomes]
rs2812310	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4742948	0.80[ASN][1000 genomes]
rs7357632	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[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	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2812297	PPP3R2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108195800-108209800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:108201000-108207600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:108201000-108209600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr9:108201600-108209800	Weak transcription	NHLF	lung
5	chr9:108203200-108207400	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr9:108203400-108208400	Enhancers	Brain Substantia Nigra	brain
7	chr9:108203600-108207400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr9:108204200-108207400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:108204200-108209800	Weak transcription	Right Ventricle	heart
10	chr9:108204400-108207800	Weak transcription	Right Atrium	heart
11	chr9:108204600-108207400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:108204600-108207400	Weak transcription	Left Ventricle	heart
13	chr9:108204600-108207600	Weak transcription	Brain Anterior Caudate	brain
14	chr9:108204600-108209200	Weak transcription	Fetal Brain Male	brain
15	chr9:108204600-108209800	Weak transcription	Liver	Liver
16	chr9:108204600-108209800	Weak transcription	Fetal Heart	heart
17	chr9:108205400-108207400	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:108205600-108208400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:108206000-108209800	Weak transcription	Psoas Muscle	Psoas
20	chr9:108206200-108208200	Enhancers	HSMM	muscle
21	chr9:108206200-108209600	Enhancers	Fetal Muscle Leg	muscle
22	chr9:108206400-108207400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:108206400-108208200	Enhancers	Brain Angular Gyrus	brain
24	chr9:108206600-108208000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:108206600-108208200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:108206600-108208200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:108206600-108208200	Enhancers	HSMMtube	muscle
28	chr9:108206600-108209600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:108206800-108207200	Weak transcription	NHDF-Ad	bronchial
30	chr9:108206800-108207400	Enhancers	HepG2	liver
31	chr9:108206800-108209200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:108206800-108209400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:108206800-108209600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:108207000-108207400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:108207000-108207400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr9:108207000-108209200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:108207000-108209400	Weak transcription	NHEK	skin
38	chr9:108207000-108209600	Weak transcription	HMEC	breast
39	chr9:108207000-108209600	Weak transcription	NH-A	brain
40	chr9:108207000-108209800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links