Variant report

Variant	rs12986587
Chromosome Location	chr2:55727476-55727477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55727452..55730813-chr2:55743534..55747364,4	K562	blood:

Variant related genes	Relation type
ENSG00000163001	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12617627	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12618859	0.88[JPT][hapmap]
rs12992408	0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12992827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12993624	0.83[JPT][hapmap]
rs12993642	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12998664	0.89[JPT][hapmap]
rs12998780	0.83[JPT][hapmap]
rs13005678	0.81[ASN][1000 genomes]
rs13009906	0.85[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs13010217	0.83[JPT][hapmap]
rs13014898	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs13015018	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs13015030	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs13015744	0.83[JPT][hapmap]
rs13022396	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13025331	0.83[JPT][hapmap]
rs13030056	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13032503	0.85[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1318672	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs17737233	0.89[JPT][hapmap]
rs1822513	0.81[CHB][hapmap]
rs2291336	0.89[JPT][hapmap]
rs35189503	0.97[ASN][1000 genomes]
rs3791654	0.83[JPT][hapmap]
rs3828238	0.89[JPT][hapmap]
rs4322879	0.83[JPT][hapmap]
rs5012561	0.81[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs55923279	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6737995	0.89[JPT][hapmap]
rs6753530	0.89[JPT][hapmap]
rs6757006	0.85[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7575170	0.80[JPT][hapmap]
rs8080	0.90[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv521318	chr2:55716650-55736704	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12986587	PRDXDD1P	cis	cerebellum	SCAN
rs12986587	PNPT1	cis	cerebellum	SCAN
rs12986587	SMEK2	cis	parietal	SCAN
rs12986587	CCDC104	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55726800-55728000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:55726800-55728000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr2:55727000-55727800	Enhancers	Osteobl	bone
4	chr2:55727000-55728000	Enhancers	NHDF-Ad	bronchial
5	chr2:55727000-55728200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:55727200-55727600	Enhancers	NH-A	brain
7	chr2:55727200-55727800	Enhancers	Hela-S3	cervix
8	chr2:55727200-55728000	Flanking Active TSS	A549	lung
9	chr2:55727200-55728000	Enhancers	HSMMtube	muscle
10	chr2:55727200-55728000	Enhancers	NHLF	lung
11	chr2:55727200-55728200	Enhancers	K562	blood
12	chr2:55727400-55727600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:55727400-55727800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:55727400-55728000	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links