Variant report

Variant	rs2643209
Chromosome Location	chr15:39005781-39005782
allele	C/T
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:12)

rs_ID	r²[population]
rs10459669	0.87[ASN][1000 genomes]
rs2624272	0.84[AFR][1000 genomes]
rs2643201	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643203	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643204	0.82[AFR][1000 genomes]
rs2643208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643215	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643216	0.84[AFR][1000 genomes]
rs3102118	0.84[AFR][1000 genomes]
rs3102119	0.81[AFR][1000 genomes]
rs55667822	0.94[ASN][1000 genomes]
rs72729402	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38999600-39006000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr15:39000600-39005800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr15:39001200-39005800	Weak transcription	NHDF-Ad	bronchial
4	chr15:39001200-39006600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:39001200-39006600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:39001200-39006600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:39001200-39006800	Weak transcription	Fetal Brain Male	brain
8	chr15:39001400-39006000	Weak transcription	HUVEC	blood vessel
9	chr15:39001400-39006400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:39001600-39005800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:39001600-39006000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:39001600-39006000	Weak transcription	HSMMtube	muscle
13	chr15:39001800-39005800	Weak transcription	NHLF	lung
14	chr15:39001800-39005800	Weak transcription	Osteobl	bone
15	chr15:39001800-39006000	Weak transcription	NH-A	brain
16	chr15:39003200-39005800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:39004600-39005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:39005600-39008400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:39005600-39008400	Enhancers	HMEC	breast
20	chr15:39005600-39008600	Enhancers	HSMM	muscle
21	chr15:39005600-39008800	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links