Variant report

Variant	rs12681417
Chromosome Location	chr8:105635003-105635004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:105633309..105635428-chr8:105716252..105717925,2	K562	blood:
2	chr8:105633597..105636250-chr8:105676084..105679408,5	K562	blood:
3	chr8:105599846..105602604-chr8:105634861..105636951,3	K562	blood:
4	chr8:105627700..105631260-chr8:105632105..105636974,7	K562	blood:
5	chr8:105598989..105604538-chr8:105634527..105638518,5	K562	blood:
6	chr8:105632918..105635015-chr8:105646007..105648866,2	K562	blood:

Variant related genes	Relation type
ENSG00000147650	Chromatin interaction
ENSG00000253350	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11987427	0.85[JPT][hapmap]
rs12541194	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12543329	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12543736	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12544422	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12546843	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs12550349	0.90[ASN][1000 genomes]
rs12674790	0.85[JPT][hapmap]
rs12680920	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298840	0.89[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap]
rs3750187	0.89[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap]
rs4461873	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4474003	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4609171	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62510142	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66479713	0.86[ASN][1000 genomes]
rs67341229	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67403507	0.86[ASN][1000 genomes]
rs6988526	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72679139	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72679149	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73295140	0.90[ASN][1000 genomes]
rs7813115	0.85[JPT][hapmap]
rs7814352	0.85[JPT][hapmap]
rs7823668	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7845549	0.85[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	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	esv2422460	chr8:105573376-105746329	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1032476	chr8:105609904-106030916	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv539710	chr8:105609904-106030916	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12681417	LRP12	cis	parietal	SCAN
rs12681417	LRP12	cis	cerebellum	SCAN
rs12681417	LRP12	cis	Skin Sun Exposed Lower leg	GTEx
rs12681417	DCAF13	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105631200-105635200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr8:105634000-105635200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr8:105634000-105635800	Flanking Active TSS	K562	blood
4	chr8:105634000-105636400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr8:105634200-105636400	Enhancers	Primary hematopoietic stem cells	blood
6	chr8:105634400-105635400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr8:105634400-105635800	Flanking Active TSS	Dnd41	blood
8	chr8:105634400-105635800	Flanking Active TSS	GM12878-XiMat	blood
9	chr8:105634400-105636800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr8:105634600-105635400	Active TSS	Fetal Thymus	thymus
11	chr8:105634600-105635600	Active TSS	Thymus	Thymus
12	chr8:105634600-105635800	Enhancers	Primary T cells from cord blood	blood
13	chr8:105634600-105636000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr8:105634800-105635200	Enhancers	NH-A	brain
15	chr8:105634800-105635400	Enhancers	HSMM	muscle
16	chr8:105634800-105635400	Enhancers	HSMMtube	muscle
17	chr8:105634800-105635800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr8:105635000-105635200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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