Variant report

Variant	rs1109380
Chromosome Location	chr2:46924490-46924491
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr2:46924402-46924773	HL-60	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46897133..46898995-chr2:46922668..46925477,2	K562	blood:
2	chr2:46923183..46926073-chr2:46944483..46946206,2	K562	blood:
3	chr2:46842180..46843861-chr2:46924432..46926384,2	K562	blood:
4	chr2:46923714..46925684-chr2:46963885..46966277,2	MCF-7	breast:
5	chr2:46915855..46917491-chr2:46923839..46925378,2	MCF-7	breast:
6	chr2:46923592..46925257-chr2:47030948..47032802,2	MCF-7	breast:
7	chr2:46919753..46923455-chr2:46923473..46925760,5	K562	blood:
8	chr2:46916264..46918533-chr2:46923065..46926019,3	K562	blood:
9	chr2:46921129..46924889-chr2:46924933..46928761,3	MCF-7	breast:

No data

Variant related genes	Relation type
SOCS5	TF binding region
ENSG00000119878	Chromatin interaction
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1058157	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11676737	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11695058	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12474201	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998753	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12998762	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12999586	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13025595	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13025984	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13429704	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17822019	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17822294	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2346878	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34401107	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35158352	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35722922	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35825831	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3829835	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4952842	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4952843	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4953419	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6738426	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7562173	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7584870	0.81[EUR][1000 genomes]
rs7594523	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs897530	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][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	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv3365634	chr2:46910377-46929000	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3460455	chr2:46910422-46928955	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv3460454	chr2:46910435-46928955	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3460456	chr2:46910436-46928951	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46911600-46924600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:46918600-46925000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:46919200-46924800	Weak transcription	A549	lung
4	chr2:46919200-46925200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:46919200-46925200	Weak transcription	NH-A	brain
6	chr2:46919400-46924800	Weak transcription	Hela-S3	cervix
7	chr2:46919800-46925000	Weak transcription	Osteobl	bone
8	chr2:46920000-46924800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr2:46920400-46925200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:46922600-46925200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:46922600-46925400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:46922800-46924600	Enhancers	HepG2	liver
13	chr2:46922800-46925000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:46922800-46925000	Weak transcription	NHDF-Ad	bronchial
15	chr2:46922800-46925000	Weak transcription	NHEK	skin
16	chr2:46922800-46925000	Weak transcription	NHLF	lung
17	chr2:46923000-46924800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:46923000-46925200	Weak transcription	HMEC	breast
19	chr2:46923800-46924800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:46924200-46925200	Enhancers	Brain Germinal Matrix	brain
21	chr2:46924400-46924800	Weak transcription	Placenta	Placenta
22	chr2:46924400-46925000	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links