Variant report

Variant	rs7863229
Chromosome Location	chr9:72618963-72618964
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1027283	0.94[ASN][1000 genomes]
rs1027284	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10735572	0.88[ASN][1000 genomes]
rs10780718	0.88[ASN][1000 genomes]
rs10780724	0.88[ASN][1000 genomes]
rs10868291	0.88[ASN][1000 genomes]
rs10868299	0.89[ASN][1000 genomes]
rs10868327	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10868358	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868378	0.94[ASN][1000 genomes]
rs1121607	0.88[ASN][1000 genomes]
rs1121608	0.88[ASN][1000 genomes]
rs1389125	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473520	0.96[ASN][1000 genomes]
rs1493046	0.85[ASN][1000 genomes]
rs1493047	0.88[ASN][1000 genomes]
rs1542769	0.94[ASN][1000 genomes]
rs1586914	0.88[ASN][1000 genomes]
rs1873825	0.90[ASN][1000 genomes]
rs1907956	0.88[ASN][1000 genomes]
rs1907959	0.88[ASN][1000 genomes]
rs2035922	0.90[ASN][1000 genomes]
rs2975859	0.94[ASN][1000 genomes]
rs2975860	0.94[ASN][1000 genomes]
rs2975926	0.93[ASN][1000 genomes]
rs3015226	0.94[ASN][1000 genomes]
rs4403478	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413835	0.94[ASN][1000 genomes]
rs4418399	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4445287	0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4487845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4490905	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4574911	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4636269	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744583	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744584	0.94[ASN][1000 genomes]
rs7019025	0.90[ASN][1000 genomes]
rs7023406	0.93[ASN][1000 genomes]
rs7025044	0.88[ASN][1000 genomes]
rs7029606	0.88[ASN][1000 genomes]
rs7035415	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7037671	0.88[ASN][1000 genomes]
rs7847934	0.88[ASN][1000 genomes]
rs7863165	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs870011	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs902964	0.92[ASN][1000 genomes]
rs931500	0.96[ASN][1000 genomes]
rs953372	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996375	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv831612	chr9:72473778-72634253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1035668	chr9:72555053-72632796	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1051004	chr9:72557761-72632015	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	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
rs7863229	MAMDC2	cis	parietal	SCAN
rs7863229	PGM5	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72612400-72619200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:72612400-72622600	Weak transcription	NHEK	skin
3	chr9:72612800-72620800	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:72618600-72619800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr9:72618600-72619800	Enhancers	HSMMtube	muscle
6	chr9:72618600-72620000	Enhancers	NHDF-Ad	bronchial
7	chr9:72618600-72620200	Enhancers	Osteobl	bone
8	chr9:72618600-72622000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:72618800-72619000	Enhancers	NH-A	brain
10	chr9:72618800-72619400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:72618800-72619800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:72618800-72620000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:72618800-72620000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:72618800-72620000	Enhancers	Fetal Lung	lung
15	chr9:72618800-72620000	Enhancers	NHLF	lung

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