Variant report

Variant	rs12887115
Chromosome Location	chr14:67990648-67990649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:67980728..67983271-chr14:67988710..67990782,2	K562	blood:
2	chr14:67980390..67986275-chr14:67988226..67995787,13	MCF-7	breast:
3	chr14:67980236..67983676-chr14:67990414..67993789,5	MCF-7	breast:
4	chr14:67984380..67986731-chr14:67988882..67991536,2	K562	blood:
5	chr14:67988568..67991154-chr14:67998353..68000955,2	MCF-7	breast:
6	chr14:67976992..67979200-chr14:67989506..67991130,2	MCF-7	breast:
7	chr14:67968272..67970276-chr14:67989655..67991450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198133	Chromatin interaction
ENSG00000054690	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10130096	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs10133618	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10134444	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10143518	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873204	0.83[ASN][1000 genomes]
rs11158675	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158676	0.83[ASN][1000 genomes]
rs11158677	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158678	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11621977	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11627207	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12878949	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12878981	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12879556	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555397	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555398	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555399	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980614	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273596	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4899206	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902477	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573776	0.81[JPT][hapmap]
rs7140327	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7140470	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7144333	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7144624	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7154258	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7155830	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7155911	0.87[GIH][hapmap];0.80[MEX][hapmap];0.80[ASN][1000 genomes]
rs7156144	0.87[GIH][hapmap];0.80[MEX][hapmap];0.80[ASN][1000 genomes]
rs7160654	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7160944	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7161368	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8011307	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8019176	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8019974	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12887115	RDH11	cis	parietal	SCAN
rs12887115	PPP2R5E	cis	cerebellum	SCAN
rs12887115	PLEKHG3	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67982600-67999000	Weak transcription	Right Atrium	heart
2	chr14:67988000-67991000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr14:67988800-67991600	Enhancers	Brain Cingulate Gyrus	brain
4	chr14:67988800-67991600	Enhancers	Brain Hippocampus Middle	brain
5	chr14:67989000-67991200	Enhancers	Brain Anterior Caudate	brain
6	chr14:67989000-67991600	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr14:67989400-67991200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:67989400-67991400	Enhancers	Brain Angular Gyrus	brain
9	chr14:67989400-67991800	Enhancers	Brain Substantia Nigra	brain
10	chr14:67989600-67990800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr14:67989600-67991600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr14:67989800-67991000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:67989800-67993000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr14:67990200-67991400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:67990200-67991400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:67990200-67991400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr14:67990600-67991800	Enhancers	Colonic Mucosa	Colon

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