Variant report

Variant	rs3761893
Chromosome Location	chr20:12990212-12990213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs2327445	0.97[ASN][1000 genomes]
rs2327447	0.97[ASN][1000 genomes]
rs2327448	0.97[ASN][1000 genomes]
rs2876238	0.97[ASN][1000 genomes]
rs360537	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs360538	0.88[EUR][1000 genomes]
rs3761895	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843768	0.97[ASN][1000 genomes]
rs3843769	0.97[ASN][1000 genomes]
rs3848762	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3848764	0.97[ASN][1000 genomes]
rs3848765	0.97[ASN][1000 genomes]
rs3848766	0.97[ASN][1000 genomes]
rs3859618	0.97[ASN][1000 genomes]
rs3966739	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4813105	0.97[ASN][1000 genomes]
rs4814179	0.83[LWK][hapmap]
rs4814181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6074546	0.97[ASN][1000 genomes]
rs6078878	0.99[ASN][1000 genomes]
rs6078880	0.99[ASN][1000 genomes]
rs6078882	0.96[ASN][1000 genomes]
rs6078883	0.97[ASN][1000 genomes]
rs6078884	0.97[ASN][1000 genomes]
rs6078885	0.97[ASN][1000 genomes]
rs6131420	0.97[ASN][1000 genomes]
rs6131421	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv833923	chr20:12904689-13064426	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3761893	PLCB4	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12988000-12997600	Weak transcription	Hela-S3	cervix
2	chr20:12989200-12990800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr20:12989200-12990800	Active TSS	Fetal Kidney	kidney
4	chr20:12989200-12991200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr20:12989200-12991400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:12989400-12990400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:12989400-12990400	Active TSS	Primary T cells from cord blood	blood
8	chr20:12989400-12990400	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr20:12989400-12990400	Active TSS	A549	lung
10	chr20:12989400-12990400	Active TSS	HMEC	breast
11	chr20:12989400-12990600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr20:12989400-12990600	Active TSS	Duodenum Mucosa	Duodenum
13	chr20:12989400-12990600	Active TSS	Stomach Smooth Muscle	stomach
14	chr20:12989400-12990600	Active TSS	HSMM	muscle
15	chr20:12989400-12990800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr20:12989400-12990800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr20:12989400-12990800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr20:12989400-12990800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr20:12989400-12990800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:12989400-12990800	Active TSS	Aorta	Aorta
21	chr20:12989400-12990800	Active TSS	Brain Angular Gyrus	brain
22	chr20:12989400-12990800	Active TSS	Brain Anterior Caudate	brain
23	chr20:12989400-12990800	Active TSS	Fetal Muscle Trunk	muscle
24	chr20:12989400-12990800	Active TSS	Placenta	Placenta
25	chr20:12989400-12990800	Active TSS	Pancreas	Pancrea
26	chr20:12989400-12990800	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr20:12989400-12990800	Active TSS	Rectal Smooth Muscle	rectum
28	chr20:12989400-12990800	Active TSS	Right Atrium	heart
29	chr20:12989400-12990800	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr20:12989400-12990800	Active TSS	NHDF-Ad	bronchial
31	chr20:12989400-12990800	Active TSS	NHLF	lung
32	chr20:12989400-12991000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr20:12989400-12992000	Active TSS	Fetal Intestine Small	intestine
34	chr20:12989400-12992600	Active TSS	Fetal Intestine Large	intestine
35	chr20:12989600-12990400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr20:12989600-12990400	Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr20:12989600-12990400	Active TSS	Liver	Liver
38	chr20:12989600-12990400	Active TSS	Right Ventricle	heart
39	chr20:12989600-12990600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr20:12989600-12990600	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr20:12989600-12990600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr20:12989600-12990600	Active TSS	Brain Cingulate Gyrus	brain
43	chr20:12989600-12990600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr20:12989600-12990600	Active TSS	Colon Smooth Muscle	Colon
45	chr20:12989600-12990600	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr20:12989600-12990600	Active TSS	Stomach Mucosa	stomach
47	chr20:12989600-12990600	Active TSS	NHEK	skin
48	chr20:12989600-12990800	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr20:12989600-12990800	Active TSS	Primary T cells fromperipheralblood	blood
50	chr20:12989600-12990800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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