Variant report

Variant	rs12338548
Chromosome Location	chr9:16564464-16564465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10116857	1.00[CEU][hapmap]
rs10117448	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10121959	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10123480	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs10123558	0.82[CEU][hapmap]
rs10511622	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10733312	1.00[CEU][hapmap]
rs10738437	0.82[CEU][hapmap]
rs10738439	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs10756763	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.94[AMR][1000 genomes]
rs10810576	0.82[CEU][hapmap]
rs10962488	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10962492	0.82[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10962493	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10962494	0.82[CEU][hapmap];0.80[MKK][hapmap]
rs10962511	1.00[CEU][hapmap];0.92[MEX][hapmap];0.80[AMR][1000 genomes]
rs12000225	1.00[ASN][1000 genomes]
rs12000228	1.00[ASN][1000 genomes]
rs12000426	0.82[AMR][1000 genomes]
rs12002297	1.00[ASN][1000 genomes]
rs12002673	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12004947	0.86[ASN][1000 genomes]
rs12335443	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12337676	1.00[CEU][hapmap]
rs12343239	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12343306	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12350242	1.00[CEU][hapmap]
rs12350853	0.82[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12352543	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1337393	1.00[CEU][hapmap]
rs1337400	1.00[CEU][hapmap]
rs1415473	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1415474	1.00[CEU][hapmap]
rs1415476	1.00[CEU][hapmap]
rs16934806	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1807023	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1927616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927617	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1927618	0.89[ASW][hapmap];0.82[CEU][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs1927626	1.00[CEU][hapmap]
rs1952345	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1952346	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs2065937	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2382808	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2382809	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2382810	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28414647	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28483319	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28593297	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602416	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28714603	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28733737	0.80[AMR][1000 genomes]
rs2891072	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56170891	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6475059	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6475060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475063	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7018594	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7021199	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022813	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7029578	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7029648	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7030387	0.92[AMR][1000 genomes]
rs7035791	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725011	1.00[CEU][hapmap]
rs73417483	1.00[ASN][1000 genomes]
rs73419403	1.00[ASN][1000 genomes]
rs7350234	1.00[CEU][hapmap]
rs7470623	1.00[CEU][hapmap]
rs7847768	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7850123	0.82[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs7856477	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap]
rs7857751	1.00[ASN][1000 genomes]
rs7858025	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861969	1.00[ASN][1000 genomes]
rs7863885	0.82[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7870380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872747	0.86[AMR][1000 genomes]
rs7872838	0.86[AMR][1000 genomes]
rs943744	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs943745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs943748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv824866	chr9:16563830-16565983	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16543800-16567000	Weak transcription	HSMMtube	muscle
2	chr9:16546000-16568400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:16551800-16567800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:16552000-16567800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:16552800-16566600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:16552800-16570200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:16552800-16571000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:16552800-16571400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:16553000-16570200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:16553000-16575200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:16556400-16566000	Weak transcription	Fetal Stomach	stomach
12	chr9:16556400-16569200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:16556400-16570600	Weak transcription	NHLF	lung
14	chr9:16556400-16575600	Weak transcription	HSMM	muscle
15	chr9:16560200-16571200	Weak transcription	Ovary	ovary
16	chr9:16560200-16571400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:16560200-16571600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:16563400-16564600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:16564200-16570600	Weak transcription	Osteobl	bone
20	chr9:16564400-16564600	Enhancers	HUES48 Cell Line	embryonic stem cell

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