Variant report

Variant	rs12894979
Chromosome Location	chr14:72716081-72716082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10131012	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10134489	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs10134542	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10143449	0.81[ASN][1000 genomes]
rs10149098	0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10150159	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10150242	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1076317	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.88[ASN][1000 genomes]
rs11847225	0.83[YRI][hapmap]
rs11848300	0.81[CEU][hapmap]
rs11851422	0.83[YRI][hapmap]
rs12148024	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12432346	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs12432632	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12883593	0.85[CEU][hapmap]
rs1402056	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1402058	0.81[CEU][hapmap]
rs1402061	0.81[CEU][hapmap]
rs1520326	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1520331	0.84[TSI][hapmap]
rs1520332	0.87[TSI][hapmap]
rs1544487	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1558071	0.82[ASN][1000 genomes]
rs1558073	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1568404	0.90[JPT][hapmap]
rs17109404	0.83[YRI][hapmap]
rs17109477	0.91[YRI][hapmap]
rs17180251	0.82[ASN][1000 genomes]
rs2079502	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2108466	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2238199	0.80[TSI][hapmap]
rs2238212	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2238213	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2238215	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2238216	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2238217	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2238218	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2238222	0.83[YRI][hapmap]
rs2238225	0.83[YRI][hapmap]
rs2238226	0.83[YRI][hapmap]
rs2238243	0.81[JPT][hapmap]
rs2238244	0.81[JPT][hapmap]
rs2239249	0.89[TSI][hapmap]
rs2239257	0.80[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2239258	0.91[JPT][hapmap]
rs2239261	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2283390	0.84[TSI][hapmap]
rs2283408	0.81[CEU][hapmap]
rs2332806	0.81[CEU][hapmap]
rs2332807	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2332808	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3784049	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4903003	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4903004	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6574055	0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs6574056	0.94[ASN][1000 genomes]
rs6574057	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7144302	0.86[JPT][hapmap]
rs7350728	0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs740337	0.83[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs763507	0.81[JPT][hapmap]
rs8006974	0.82[YRI][hapmap]
rs8007922	0.83[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs847241	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs847304	0.88[ASN][1000 genomes]
rs847345	0.91[JPT][hapmap]
rs847354	0.86[GIH][hapmap];0.89[TSI][hapmap]
rs847359	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1041492	chr14:72634606-72768970	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12894979	OSGIN2	trans	cerebellum	SCAN
rs12894979	VTI1B	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72699800-72719600	Weak transcription	Right Ventricle	heart
2	chr14:72706600-72721200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:72711600-72719600	Weak transcription	Left Ventricle	heart
4	chr14:72712000-72722200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr14:72712800-72722600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr14:72715400-72716200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr14:72715400-72716400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr14:72715400-72716400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr14:72715400-72716600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr14:72715800-72716200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr14:72715800-72716200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr14:72715800-72716200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr14:72715800-72717200	Weak transcription	Fetal Heart	heart
14	chr14:72716000-72717200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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