Variant report

Variant	rs12880679
Chromosome Location	chr14:72583802-72583803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11158949	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12434682	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12880020	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12881966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17107825	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17179706	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2190628	0.81[LWK][hapmap]
rs2238259	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2238260	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283417	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283418	0.94[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4902987	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4902988	0.83[EUR][1000 genomes]
rs67722975	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8004062	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs981975	0.82[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv902076	chr14:72565656-72632217	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv902077	chr14:72576679-72632217	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv902078	chr14:72581575-72628433	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv902079	chr14:72583802-72632217	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12880679	C14orf115	cis	parietal	SCAN
rs12880679	ACYP1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72566600-72591800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:72581200-72584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:72583800-72584200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr14:72583800-72584400	Enhancers	Left Ventricle	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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