Variant report

Variant	rs3759664
Chromosome Location	chr14:55371579-55371580
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	chr14:55030801..55036234-chr14:55366700..55372024,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000020577	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10136972	0.82[ASN][1000 genomes]
rs10137071	0.82[ASN][1000 genomes]
rs10140164	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs10143038	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10149103	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1107960	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs1107961	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11158028	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11621165	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11621177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11626396	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11627963	0.93[EUR][1000 genomes]
rs11629355	0.94[EUR][1000 genomes]
rs11847771	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11852045	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12587434	0.83[CEU][hapmap]
rs17128052	0.95[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17128120	0.86[JPT][hapmap]
rs17253633	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes]
rs2149482	0.82[ASN][1000 genomes]
rs2878172	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs2878174	0.86[JPT][hapmap]
rs34544088	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759662	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759663	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759665	0.82[ASN][1000 genomes]
rs3783641	0.95[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45459500	0.93[EUR][1000 genomes]
rs55704705	0.83[EUR][1000 genomes]
rs55726650	0.94[EUR][1000 genomes]
rs55751189	0.95[EUR][1000 genomes]
rs56188649	0.93[EUR][1000 genomes]
rs56213135	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57095876	0.83[ASN][1000 genomes]
rs57622454	0.93[EUR][1000 genomes]
rs59074935	0.93[EUR][1000 genomes]
rs60258834	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61709472	0.95[EUR][1000 genomes]
rs7146285	0.86[JPT][hapmap]
rs7147201	0.95[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72713482	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72715547	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72715552	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72715575	0.93[EUR][1000 genomes]
rs8006363	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8006568	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8007267	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8008858	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8010570	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8011358	0.95[EUR][1000 genomes]
rs8012152	0.86[JPT][hapmap]
rs8017210	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8018688	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8019390	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs8019824	0.81[ASN][1000 genomes]
rs8020545	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs8022049	0.86[JPT][hapmap]
rs8022453	0.93[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8023187	0.91[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs943913	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv3358123	chr14:55359251-55378030	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3759664	LGALS3	cis	parietal	SCAN
rs3759664	FBXO34	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55370000-55373600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr14:55370200-55372800	Weak transcription	GM12878-XiMat	blood
3	chr14:55370200-55374600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr14:55370200-55374800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr14:55370200-55376800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr14:55370400-55371600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr14:55370400-55371600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr14:55370400-55371600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr14:55370400-55374400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr14:55370400-55374600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr14:55370400-55374600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr14:55370400-55374600	Weak transcription	Dnd41	blood
13	chr14:55370400-55374800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr14:55370400-55374800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:55370600-55371600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr14:55370600-55374600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr14:55370600-55388600	Weak transcription	HepG2	liver

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