Variant report

Variant	rs11789339
Chromosome Location	chr9:12741529-12741530
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10960766	0.93[EUR][1000 genomes]
rs10960767	0.93[EUR][1000 genomes]
rs10960768	0.93[EUR][1000 genomes]
rs11787674	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11787999	0.90[EUR][1000 genomes]
rs11788192	0.93[EUR][1000 genomes]
rs11789481	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11789805	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11791137	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11791392	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11791497	0.85[EUR][1000 genomes]
rs11791954	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11793178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11793280	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11794050	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11794202	0.93[EUR][1000 genomes]
rs11795082	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12001299	0.93[EUR][1000 genomes]
rs12001737	0.93[EUR][1000 genomes]
rs12001745	0.93[EUR][1000 genomes]
rs12001885	0.93[EUR][1000 genomes]
rs12001964	0.93[EUR][1000 genomes]
rs12005881	0.93[EUR][1000 genomes]
rs16929383	0.90[EUR][1000 genomes]
rs16929385	0.90[EUR][1000 genomes]
rs16929391	0.90[EUR][1000 genomes]
rs16929400	0.88[EUR][1000 genomes]
rs16929473	0.93[EUR][1000 genomes]
rs17280279	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17280629	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17346748	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2209278	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34509359	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35238630	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35852762	0.93[EUR][1000 genomes]
rs35866166	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3891858	0.88[EUR][1000 genomes]
rs41306290	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41314571	1.00[AFR][1000 genomes]
rs61758391	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61758394	0.88[EUR][1000 genomes]
rs62638049	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7025241	0.93[EUR][1000 genomes]
rs7025758	0.93[EUR][1000 genomes]
rs7026121	0.93[EUR][1000 genomes]
rs7026199	0.93[EUR][1000 genomes]
rs7030751	0.98[EUR][1000 genomes]
rs7033962	0.98[EUR][1000 genomes]
rs7040346	0.90[EUR][1000 genomes]
rs7041590	0.93[EUR][1000 genomes]
rs7041735	0.93[EUR][1000 genomes]
rs71507329	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73402088	0.93[EUR][1000 genomes]
rs73402092	0.93[EUR][1000 genomes]
rs768617	0.90[EUR][1000 genomes]
rs7875424	0.90[EUR][1000 genomes]
rs7876041	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv613613	chr9:12641987-12773263	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	esv2757318	chr9:12721881-12758881	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv8420	chr9:12725200-12750151	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv3693020	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv818690	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv516527	chr9:12738690-12748486	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12740400-12741600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:12741400-12748400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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