Variant report

Variant	rs3748386
Chromosome Location	chr16:69974659-69974660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69969820..69971690-chr16:69974264..69975931,2	K562	blood:
2	chr16:69967047..69970080-chr16:69972190..69975168,3	MCF-7	breast:
3	chr16:69970218..69972832-chr16:69974384..69976612,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11866381	0.88[CEU][hapmap]
rs12930433	0.87[CEU][hapmap];0.88[YRI][hapmap]
rs2270843	0.85[JPT][hapmap]
rs2868017	0.93[YRI][hapmap]
rs3748387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748389	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]
rs4985392	0.82[LWK][hapmap];0.93[YRI][hapmap]
rs57258715	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6499285	0.93[YRI][hapmap]
rs6499292	0.87[CEU][hapmap];0.80[CHB][hapmap];0.85[YRI][hapmap]
rs66717971	0.84[EUR][1000 genomes]
rs7190012	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7206524	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9939092	0.88[CEU][hapmap];0.80[CHB][hapmap];0.92[YRI][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3748386	WWP2	cis	cerebellum	SCAN
rs3748386	WWP2	cis	parietal	SCAN
rs3748386	CLEC18C	cis	Whole Blood	GTEx
rs3748386	PDPR	cis	parietal	SCAN
rs3748386	LOC283970	cis	multi-tissue	Pritchard
rs3748386	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs3748386	PDPR	cis	cerebellum	SCAN
rs3748386	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69947600-69977200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr16:69948200-69977400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr16:69948400-69977400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr16:69952600-69976000	Weak transcription	Hela-S3	cervix
5	chr16:69953600-69974800	Weak transcription	A549	lung
6	chr16:69954400-69976000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:69956400-69975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:69957400-69977400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr16:69957600-69975400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr16:69957800-69977200	Strong transcription	Fetal Intestine Small	intestine
11	chr16:69959000-69976400	Strong transcription	Thymus	Thymus
12	chr16:69959000-69977200	Strong transcription	Fetal Intestine Large	intestine
13	chr16:69959000-69977600	Strong transcription	Primary T cells from cord blood	blood
14	chr16:69959200-69975400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr16:69959400-69976200	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr16:69959600-69975200	Strong transcription	Fetal Thymus	thymus
17	chr16:69959600-69975600	Strong transcription	Fetal Stomach	stomach
18	chr16:69961400-69976600	Weak transcription	Right Atrium	heart
19	chr16:69961400-69977000	Weak transcription	HSMM	muscle
20	chr16:69961600-69974800	Weak transcription	Psoas Muscle	Psoas
21	chr16:69961600-69976800	Strong transcription	Spleen	Spleen
22	chr16:69962200-69975200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr16:69962400-69976800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr16:69962400-69976800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr16:69962600-69976800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr16:69962800-69975200	Strong transcription	Lung	lung
27	chr16:69962800-69975400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr16:69962800-69975800	Strong transcription	Colonic Mucosa	Colon
29	chr16:69962800-69975800	Strong transcription	Pancreas	Pancrea
30	chr16:69962800-69976200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr16:69962800-69976200	Strong transcription	Gastric	stomach
32	chr16:69963200-69975200	Strong transcription	NHLF	lung
33	chr16:69963200-69975400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr16:69963200-69975800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr16:69963200-69976600	Strong transcription	Fetal Brain Female	brain
36	chr16:69963200-69977000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr16:69963400-69975000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr16:69963400-69975800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr16:69963400-69976000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr16:69963400-69977200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr16:69963600-69975000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr16:69963600-69976400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr16:69963800-69975200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr16:69963800-69975400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr16:69963800-69976200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:69964000-69974800	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr16:69964000-69975000	Strong transcription	Adipose Nuclei	Adipose
48	chr16:69964200-69975000	Strong transcription	Left Ventricle	heart
49	chr16:69964200-69975200	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr16:69964200-69976000	Strong transcription	Osteobl	bone

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