Variant report

Variant	rs12346701
Chromosome Location	chr9:977662-977663
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12346410	0.90[AFR][1000 genomes]
rs72701085	0.83[AFR][1000 genomes]
rs72701088	0.92[AFR][1000 genomes]
rs72701089	0.92[AFR][1000 genomes]
rs72701091	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025492	chr9:478813-1157169	Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv539897	chr9:478813-1157169	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv429977	chr9:584087-983301	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription 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 miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv613037	chr9:643453-1138368	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817248	chr9:706283-1457665	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv892010	chr9:841152-1069663	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1034070	chr9:911265-1152351	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2755928	chr9:924525-985979	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv892013	chr9:943611-1047343	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1018926	chr9:965006-1014141	Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv892014	chr9:972476-1032153	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3408115	chr9:975477-978825	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:974400-977800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr9:975400-978800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:976000-977800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr9:976000-977800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr9:976000-977800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:976000-977800	Bivalent Enhancer	Fetal Stomach	stomach
7	chr9:976200-977800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:976200-977800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:976200-977800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr9:976200-977800	Bivalent Enhancer	Fetal Brain Male	brain
11	chr9:976200-977800	Bivalent Enhancer	Spleen	Spleen
12	chr9:976200-978000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr9:976400-977800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:976400-977800	Bivalent Enhancer	Lung	lung
15	chr9:976400-978000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
16	chr9:976400-978600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
17	chr9:976600-977800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:976600-977800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:976800-977800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
20	chr9:977200-977800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
21	chr9:977200-977800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
22	chr9:977400-977800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr9:977400-977800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
24	chr9:977400-977800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
25	chr9:977400-977800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr9:977400-977800	Bivalent Enhancer	Placenta	Placenta
27	chr9:977400-978000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
28	chr9:977400-978000	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr9:977600-977800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr9:977600-977800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
31	chr9:977600-977800	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr9:977600-977800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
33	chr9:977600-977800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
34	chr9:977600-978400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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