Variant report

Variant	rs2378971
Chromosome Location	chr14:32370206-32370207
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	chr14:32369516..32371564-chr14:32376698..32378777,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12147853	0.80[ASN][1000 genomes]
rs1278866	0.88[ASN][1000 genomes]
rs1278867	0.88[ASN][1000 genomes]
rs1278868	0.88[ASN][1000 genomes]
rs12878699	0.88[ASN][1000 genomes]
rs12897964	0.88[ASN][1000 genomes]
rs1953271	0.93[ASN][1000 genomes]
rs1953272	0.90[ASN][1000 genomes]
rs1953273	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1963748	0.90[ASN][1000 genomes]
rs34855165	0.88[ASN][1000 genomes]
rs35304997	0.87[ASN][1000 genomes]
rs4981926	0.89[ASN][1000 genomes]
rs4981927	0.90[ASN][1000 genomes]
rs4981928	0.84[ASN][1000 genomes]
rs55890730	0.85[ASN][1000 genomes]
rs56232824	0.88[ASN][1000 genomes]
rs57516226	0.88[ASN][1000 genomes]
rs8008105	0.87[ASN][1000 genomes]
rs8008595	0.83[ASN][1000 genomes]
rs8009593	0.83[ASN][1000 genomes]
rs8016828	0.82[ASN][1000 genomes]

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	nsv564182	chr14:32110519-32584337	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046526	chr14:32110537-32567426	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv526200	chr14:32308511-32454372	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv519917	chr14:32363980-32375359	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2760330	chr14:32364547-32377760	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1040337	chr14:32364547-32387656	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2378971	GKAP1	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:32364200-32371200	Weak transcription	Placenta	Placenta
2	chr14:32364400-32371000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr14:32364800-32370400	Weak transcription	K562	blood
4	chr14:32364800-32371000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:32365200-32370800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr14:32365200-32370800	Weak transcription	NHEK	skin
7	chr14:32367200-32370800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:32367200-32376200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr14:32368400-32370400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr14:32368600-32370800	Weak transcription	HMEC	breast
11	chr14:32370000-32370800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr14:32370200-32370600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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