Variant report

Variant	rs2676071
Chromosome Location	chr15:33597076-33597077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12148576	0.81[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.96[ASN][1000 genomes]
rs1567847	0.84[AMR][1000 genomes]
rs2670942	0.92[ASN][1000 genomes]
rs2670945	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2670946	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2670947	0.84[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2676072	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2676073	0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2676075	0.83[MEX][hapmap];0.88[TSI][hapmap]
rs2676077	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2676084	0.88[ASN][1000 genomes]
rs907953	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv482299	chr15:33449137-33624122	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv533346	chr15:33469439-33809641	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv832963	chr15:33514798-33712442	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Periodontitis (Mean PAL)	24024966	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2676071	RP11-489D6.2	cis	Esophagus Muscularis	GTEx
rs2676071	RP11-489D6.2	cis	Muscle Skeletal	GTEx
rs2676071	RP11-489D6.2	cis	Artery Aorta	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33590200-33597200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:33596200-33598000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr15:33596400-33597600	Enhancers	Brain Substantia Nigra	brain
4	chr15:33596400-33597800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr15:33596400-33597800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:33596400-33597800	Enhancers	Brain Hippocampus Middle	brain
7	chr15:33596400-33601600	Weak transcription	Aorta	Aorta
8	chr15:33596600-33597200	Enhancers	Brain Cingulate Gyrus	brain
9	chr15:33596800-33597400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:33596800-33597800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr15:33596800-33598000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr15:33596800-33598000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr15:33597000-33597800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr15:33597000-33598200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:33597000-33602200	Weak transcription	Brain Anterior Caudate	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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