Variant report

Variant	rs12880425
Chromosome Location	chr14:97203041-97203042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10136975	0.85[ASN][1000 genomes]
rs10139694	0.85[ASN][1000 genomes]
rs10143101	0.86[ASN][1000 genomes]
rs10143369	0.85[ASN][1000 genomes]
rs10146854	0.90[ASN][1000 genomes]
rs11160362	0.86[ASN][1000 genomes]
rs11160363	0.85[ASN][1000 genomes]
rs11629293	0.83[ASN][1000 genomes]
rs12147403	0.85[ASN][1000 genomes]
rs12434260	0.85[ASN][1000 genomes]
rs12895746	0.88[ASN][1000 genomes]
rs17094398	0.87[ASN][1000 genomes]
rs17094403	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28670537	0.88[ASN][1000 genomes]
rs2887581	0.88[ASN][1000 genomes]
rs34142794	0.85[ASN][1000 genomes]
rs34344944	0.82[ASN][1000 genomes]
rs35981455	0.82[ASN][1000 genomes]
rs4243716	0.88[ASN][1000 genomes]
rs4578584	0.81[ASN][1000 genomes]
rs59880225	0.82[ASN][1000 genomes]
rs66487336	0.85[ASN][1000 genomes]
rs71415050	0.88[ASN][1000 genomes]
rs7157651	0.84[ASN][1000 genomes]
rs737209	0.86[ASN][1000 genomes]
rs8009078	0.82[ASN][1000 genomes]
rs8012361	0.82[ASN][1000 genomes]
rs8014262	0.82[ASN][1000 genomes]
rs8015493	0.88[ASN][1000 genomes]
rs872954	0.84[JPT][hapmap]
rs912343	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048302	chr14:97000845-97250538	Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1041078	chr14:97001679-97279220	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1050075	chr14:97004951-97279220	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1044202	chr14:97155291-97683983	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv542179	chr14:97155291-97683983	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12880425	CCNK	cis	cerebellum	SCAN
rs12880425	TRIP11	cis	cerebellum	SCAN
rs12880425	CHGA	cis	cerebellum	SCAN
rs12880425	VRK1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:97199200-97206000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:97201800-97203600	Flanking Active TSS	Brain Germinal Matrix	brain
3	chr14:97202000-97207400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:97202200-97203400	Flanking Active TSS	Fetal Brain Female	brain
5	chr14:97202600-97204200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr14:97202600-97204600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr14:97202800-97203200	Bivalent Enhancer	Fetal Kidney	kidney
8	chr14:97203000-97203200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
9	chr14:97203000-97203200	Flanking Active TSS	Fetal Brain Male	brain
10	chr14:97203000-97203400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr14:97203000-97203600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr14:97203000-97205800	Enhancers	HUES48 Cell Line	embryonic stem cell

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