Variant report

Variant	rs2283399
Chromosome Location	chr14:72722032-72722033
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	chr14:72720189..72722386-chr14:72732098..72734975,2	K562	blood:
2	chr14:72711994..72714695-chr14:72721324..72722948,2	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs11847225	0.82[CEU][hapmap]
rs11851422	0.82[CEU][hapmap]
rs12147219	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12147220	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12147238	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12147792	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12147803	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12881198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12883470	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12891167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12897241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1520329	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1589301	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17109194	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17109324	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17109573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17109589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17110829	0.93[AMR][1000 genomes]
rs1879288	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1981604	0.81[AMR][1000 genomes]
rs2079501	0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs2238200	0.90[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2238203	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2238208	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2238209	0.89[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2238210	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2238219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238221	0.80[JPT][hapmap]
rs2238223	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238224	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238225	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs2238226	0.82[CEU][hapmap]
rs2238228	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238229	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238230	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238231	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238232	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238233	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238234	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238235	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238236	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238237	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238239	0.90[CEU][hapmap];0.93[AFR][1000 genomes]
rs2238240	0.90[CEU][hapmap]
rs2239252	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2239253	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2239254	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2239256	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs2239260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2239262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283394	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2283395	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2283400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34122902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34373542	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34755616	0.93[AMR][1000 genomes]
rs34905590	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35133217	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs35291137	0.93[AMR][1000 genomes]
rs35367207	0.93[AFR][1000 genomes]
rs35413081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35953744	0.82[AFR][1000 genomes]
rs36162266	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4324071	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4899429	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4899431	0.93[AMR][1000 genomes]
rs4899432	0.93[AMR][1000 genomes]
rs4903000	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4903005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4903011	0.93[AMR][1000 genomes]
rs55954287	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56263585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66507723	0.93[AMR][1000 genomes]
rs66823874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67838629	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs699359	0.80[ASN][1000 genomes]
rs7156265	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7156404	0.84[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs722561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72721816	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8006974	0.80[CEU][hapmap]
rs8013850	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8015237	0.93[AMR][1000 genomes]
rs8016936	0.82[CEU][hapmap]
rs847246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs847247	0.89[ASN][1000 genomes]
rs847248	0.82[ASN][1000 genomes]
rs847249	0.81[ASN][1000 genomes]
rs847251	0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs847256	0.92[ASN][1000 genomes]
rs847257	0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs847260	0.83[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs847261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2283399	PTHLH	trans	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72712000-72722200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:72712800-72722600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr14:72719600-72723000	Enhancers	Placenta	Placenta
4	chr14:72721800-72723200	Weak transcription	Fetal Heart	heart
5	chr14:72722000-72722800	Weak transcription	Left Ventricle	heart
6	chr14:72722000-72726000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr14:72722000-72727800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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