Variant report

Variant	rs12406609
Chromosome Location	chr1:46983921-46983922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46945158..46947709-chr1:46983421..46985167,2	K562	blood:
2	chr1:46981951..46984222-chr1:46986722..46989512,3	MCF-7	breast:
3	chr1:46945406..46947709-chr1:46983667..46986357,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12401610	1.00[AMR][1000 genomes]
rs12405092	0.80[AMR][1000 genomes]
rs12405620	1.00[AMR][1000 genomes]
rs12410292	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57552288	1.00[AMR][1000 genomes]
rs58174810	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS 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
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1010578	chr1:46977818-47010579	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46972800-46986000	Weak transcription	Right Atrium	heart
2	chr1:46981200-46984200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:46981600-46984200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:46981800-46984000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:46981800-46984000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:46981800-46984000	Enhancers	Esophagus	oesophagus
7	chr1:46981800-46984400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:46981800-46986200	Enhancers	A549	lung
9	chr1:46981800-46986800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:46982200-46984200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:46982200-46984200	Enhancers	Fetal Intestine Small	intestine
12	chr1:46982200-46984200	Enhancers	Stomach Mucosa	stomach
13	chr1:46982200-46984200	Flanking Active TSS	Hela-S3	cervix
14	chr1:46982600-46986000	Weak transcription	Gastric	stomach
15	chr1:46982800-46984200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr1:46983000-46984200	Enhancers	HepG2	liver
17	chr1:46983000-46984400	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr1:46983200-46984000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
19	chr1:46983200-46984000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
20	chr1:46983200-46984200	Enhancers	H9 Cell Line	embryonic stem cell
21	chr1:46983200-46984400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
22	chr1:46983200-46984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:46983200-46985800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:46983200-46986000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:46983200-46987800	Weak transcription	Pancreas	Pancrea
26	chr1:46983200-46989800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:46983400-46984000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
28	chr1:46983400-46984000	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:46983400-46984200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
30	chr1:46983400-46984200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:46983400-46984800	Weak transcription	NHEK	skin
32	chr1:46983400-46985000	Weak transcription	HMEC	breast
33	chr1:46983400-46985600	Weak transcription	HSMMtube	muscle
34	chr1:46983400-46985800	Enhancers	K562	blood
35	chr1:46983600-46984200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr1:46983800-46984000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:46983800-46984000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:46983800-46984000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
39	chr1:46983800-46984000	Enhancers	Spleen	Spleen

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