Variant report

Variant	rs3748389
Chromosome Location	chr16:69973825-69973826
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	chr16:69967047..69970080-chr16:69972190..69975168,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11866381	0.83[CEU][hapmap]
rs12930433	0.83[CEU][hapmap]
rs2270843	0.85[JPT][hapmap]
rs3748386	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748387	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57258715	0.83[EUR][1000 genomes]
rs6499292	0.83[CEU][hapmap];0.80[CHB][hapmap];0.85[YRI][hapmap]
rs66717971	0.82[EUR][1000 genomes]
rs7190012	0.80[EUR][1000 genomes]
rs7206524	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9939092	0.83[CEU][hapmap];0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv1792580	chr16:69950347-70005207	Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	esv1801278	chr16:69951043-70050770	Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	esv1829103	chr16:69951043-70050770	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
10	nsv1853	chr16:69962296-70268856	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
11	esv1824931	chr16:69968850-70230516	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv1829372	chr16:69968850-70230516	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	esv1830874	chr16:69968850-70298988	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
14	esv15512	chr16:69970836-70032614	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
15	esv2754644	chr16:69971965-70191118	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3748389	WWP2	cis	parietal	SCAN
rs3748389	PDPR	cis	parietal	SCAN
rs3748389	SF3B3	cis	cerebellum	SCAN
rs3748389	PDPR	cis	cerebellum	SCAN
rs3748389	CLEC18C	cis	Whole Blood	GTEx
rs3748389	WWP2	cis	cerebellum	SCAN
rs3748389	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
2	chr16:69947600-69977200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr16:69948200-69977400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr16:69948400-69977400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr16:69952600-69976000	Weak transcription	Hela-S3	cervix
6	chr16:69953600-69974800	Weak transcription	A549	lung
7	chr16:69954400-69976000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr16:69956400-69975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr16:69957400-69977400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr16:69957600-69975400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr16:69957800-69977200	Strong transcription	Fetal Intestine Small	intestine
12	chr16:69959000-69976400	Strong transcription	Thymus	Thymus
13	chr16:69959000-69977200	Strong transcription	Fetal Intestine Large	intestine
14	chr16:69959000-69977600	Strong transcription	Primary T cells from cord blood	blood
15	chr16:69959200-69975400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr16:69959400-69976200	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr16:69959600-69975200	Strong transcription	Fetal Thymus	thymus
18	chr16:69959600-69975600	Strong transcription	Fetal Stomach	stomach
19	chr16:69961400-69976600	Weak transcription	Right Atrium	heart
20	chr16:69961400-69977000	Weak transcription	HSMM	muscle
21	chr16:69961600-69974800	Weak transcription	Psoas Muscle	Psoas
22	chr16:69961600-69976800	Strong transcription	Spleen	Spleen
23	chr16:69962200-69975200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr16:69962400-69976800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr16:69962400-69976800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr16:69962600-69976800	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr16:69962800-69974600	Strong transcription	HepG2	liver
28	chr16:69962800-69975200	Strong transcription	Lung	lung
29	chr16:69962800-69975400	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr16:69962800-69975800	Strong transcription	Colonic Mucosa	Colon
31	chr16:69962800-69975800	Strong transcription	Pancreas	Pancrea
32	chr16:69962800-69976200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr16:69962800-69976200	Strong transcription	Gastric	stomach
34	chr16:69963200-69974600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr16:69963200-69975200	Strong transcription	NHLF	lung
36	chr16:69963200-69975400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr16:69963200-69975800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr16:69963200-69976600	Strong transcription	Fetal Brain Female	brain
39	chr16:69963200-69977000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr16:69963400-69975000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr16:69963400-69975800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr16:69963400-69976000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr16:69963400-69977200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr16:69963600-69974400	Strong transcription	Rectal Smooth Muscle	rectum
45	chr16:69963600-69975000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr16:69963600-69976400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr16:69963800-69975200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr16:69963800-69975400	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr16:69963800-69976200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr16:69964000-69974800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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