Variant report

Variant	rs17109573
Chromosome Location	chr14:72700902-72700903
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	chr14:72576115..72579038-chr14:72700345..72702644,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11847225	0.82[CEU][hapmap]
rs11851422	0.82[CEU][hapmap]
rs12147219	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12147220	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12147238	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12147792	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12147803	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12881198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12883470	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12891167	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]
rs12897241	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]
rs1520327	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1520329	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1589301	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17109194	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17109324	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17109589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1879288	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2079501	0.83[JPT][hapmap]
rs2238200	0.90[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2238203	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2238208	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2238209	0.89[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2238210	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2238219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238221	0.80[JPT][hapmap]
rs2238223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2238224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2238225	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs2238226	0.82[CEU][hapmap]
rs2238228	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2238229	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2238230	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2238231	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2238232	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2238233	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2238234	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2238235	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2238236	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2238237	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2238239	0.90[CEU][hapmap];0.93[AFR][1000 genomes]
rs2238240	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs2239252	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2239253	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2239254	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2239256	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs2239260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2239262	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]
rs2283394	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2283395	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2283399	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]
rs2283400	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34122902	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34373542	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34905590	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35133217	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs35367207	0.93[AFR][1000 genomes]
rs35413081	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35953744	0.82[AFR][1000 genomes]
rs36162266	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4324071	0.84[EUR][1000 genomes]
rs4899429	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4903000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4903005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55954287	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56263585	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66823874	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67838629	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs699359	0.82[ASN][1000 genomes]
rs7156265	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7156404	0.84[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs722561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72721816	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8006974	0.80[CEU][hapmap]
rs8013850	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8016936	0.82[CEU][hapmap]
rs847246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs847247	0.90[ASN][1000 genomes]
rs847248	0.84[ASN][1000 genomes]
rs847249	0.83[ASN][1000 genomes]
rs847251	0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs847256	0.94[ASN][1000 genomes]
rs847257	0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs847260	0.83[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs847261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv977614	chr14:72696106-72702781	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17109573	PTHLH	trans	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72687800-72705800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:72699800-72719600	Weak transcription	Right Ventricle	heart
3	chr14:72700600-72709800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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