Variant report

Variant	rs13413584
Chromosome Location	chr2:40265654-40265655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:40265649-40266385	SK-N-SH	brain:	n/a	chr2:40266056-40266064

Variant related genes	Relation type
SLC8A1-AS1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10171694	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181405	1.00[AMR][1000 genomes]
rs10181487	1.00[AMR][1000 genomes]
rs10188252	1.00[ASW][hapmap]
rs13391265	1.00[AMR][1000 genomes]
rs13397627	1.00[ASW][hapmap]
rs13404003	1.00[AMR][1000 genomes]
rs13431212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544276	1.00[AMR][1000 genomes]
rs6544295	1.00[AMR][1000 genomes]
rs7425096	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	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv873899	chr2:40161168-40281964	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1009532	chr2:40165606-40291224	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv535653	chr2:40165606-40291224	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873900	chr2:40202505-40278909	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv581501	chr2:40256218-40285145	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40262000-40265800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:40262200-40265800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:40262200-40265800	Weak transcription	NHDF-Ad	bronchial
4	chr2:40262200-40268600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:40262400-40269000	Weak transcription	HMEC	breast
6	chr2:40262600-40266000	Weak transcription	Dnd41	blood
7	chr2:40262800-40270200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:40262800-40270200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:40264200-40266000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:40264400-40267200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:40264600-40265800	Weak transcription	HSMMtube	muscle
12	chr2:40264800-40267000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr2:40264800-40270600	Weak transcription	Right Atrium	heart
14	chr2:40265000-40267600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:40265000-40268800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr2:40265400-40268600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:40265400-40270600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:40265600-40265800	Enhancers	Fetal Muscle Trunk	muscle
19	chr2:40265600-40265800	Enhancers	Left Ventricle	heart
20	chr2:40265600-40266000	Enhancers	NHLF	lung
21	chr2:40265600-40266200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:40265600-40266400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:40265600-40266400	Enhancers	Colon Smooth Muscle	Colon
24	chr2:40265600-40266400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr2:40265600-40266600	Enhancers	Fetal Stomach	stomach
26	chr2:40265600-40267200	Enhancers	Osteobl	bone
27	chr2:40265600-40268800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:40265600-40270200	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links