Variant report

Variant	rs718364
Chromosome Location	chr14:39909547-39909548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39900954..39903796-chr14:39908500..39911115,2	MCF-7	breast:
2	chr14:39903003..39906043-chr14:39907787..39910140,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165355	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10143351	0.84[AFR][1000 genomes]
rs10145949	0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs10872920	0.82[JPT][hapmap]
rs11157053	0.82[JPT][hapmap]
rs11621330	0.82[JPT][hapmap]
rs12050477	0.87[ASN][1000 genomes]
rs12232110	0.80[ASN][1000 genomes]
rs12434140	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs12587625	0.87[ASN][1000 genomes]
rs12588110	0.85[ASN][1000 genomes]
rs12588175	0.87[ASN][1000 genomes]
rs12588483	0.87[ASN][1000 genomes]
rs12590172	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12880644	0.85[ASN][1000 genomes]
rs12882250	0.85[ASN][1000 genomes]
rs12883652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886696	0.80[ASN][1000 genomes]
rs12886769	0.85[ASN][1000 genomes]
rs12894855	0.95[CHB][hapmap]
rs12897960	0.85[ASN][1000 genomes]
rs17109296	0.87[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1807940	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1950330	0.81[ASN][1000 genomes]
rs1950331	0.80[ASN][1000 genomes]
rs1950333	0.80[ASN][1000 genomes]
rs1950335	0.80[ASN][1000 genomes]
rs1950336	0.84[ASN][1000 genomes]
rs1950338	0.87[ASN][1000 genomes]
rs1950952	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1955726	0.80[ASN][1000 genomes]
rs1955729	0.87[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2038278	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082635	0.82[JPT][hapmap]
rs2207291	0.84[ASN][1000 genomes]
rs2207293	0.80[ASN][1000 genomes]
rs2274395	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2415545	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs2415549	0.87[ASN][1000 genomes]
rs2415550	0.84[ASN][1000 genomes]
rs2899889	0.80[ASN][1000 genomes]
rs34649642	0.84[ASN][1000 genomes]
rs35459433	0.87[ASN][1000 genomes]
rs35553183	0.85[ASN][1000 genomes]
rs35693868	0.84[ASN][1000 genomes]
rs35708308	0.82[ASN][1000 genomes]
rs36010374	0.84[ASN][1000 genomes]
rs3814860	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4899245	0.85[ASN][1000 genomes]
rs4902528	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[TSI][hapmap]
rs4902569	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs4902570	0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs4902598	0.84[ASN][1000 genomes]
rs4902599	0.84[ASN][1000 genomes]
rs4902622	0.87[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4902636	0.84[ASN][1000 genomes]
rs4902637	0.84[ASN][1000 genomes]
rs4902648	0.83[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4902665	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4902676	0.83[ASN][1000 genomes]
rs56046902	0.84[ASN][1000 genomes]
rs6571919	0.82[JPT][hapmap]
rs71407788	0.84[ASN][1000 genomes]
rs71407789	0.84[ASN][1000 genomes]
rs7140983	0.83[ASN][1000 genomes]
rs7148377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152341	0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7152935	0.87[ASN][1000 genomes]
rs7153413	0.87[ASN][1000 genomes]
rs7160664	0.87[AFR][1000 genomes]
rs7161403	0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs719455	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs72675487	0.82[ASN][1000 genomes]
rs8003397	0.84[ASN][1000 genomes]
rs8003621	0.85[ASN][1000 genomes]
rs8006123	0.85[ASN][1000 genomes]
rs8006321	0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs8006893	0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs8011173	0.81[ASW][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap]
rs8018717	0.82[JPT][hapmap]
rs8019328	0.93[ASW][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs910370	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs910371	0.84[ASN][1000 genomes]
rs9332387	0.87[ASN][1000 genomes]
rs956109	0.82[JPT][hapmap]

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	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv832774	chr14:39897746-40060823	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs718364	LRFN5	cis	cerebellum	SCAN
rs718364	CTAGE5	cis	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39902400-39910200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:39902400-39911400	Weak transcription	Gastric	stomach
3	chr14:39902800-39910200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:39903000-39910000	Weak transcription	Lung	lung
5	chr14:39903000-39910800	Weak transcription	Fetal Brain Male	brain
6	chr14:39903000-39911200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr14:39903000-39912600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:39903000-39916400	Weak transcription	Fetal Heart	heart
9	chr14:39903200-39910800	Weak transcription	Brain Hippocampus Middle	brain
10	chr14:39903200-39912000	Weak transcription	Aorta	Aorta
11	chr14:39908600-39910400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr14:39909400-39909800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr14:39909400-39910200	Weak transcription	Brain Anterior Caudate	brain

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