Variant report

Variant	rs11926040
Chromosome Location	chr3:145962692-145962693
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	chr3:145956753..145960171-chr3:145962648..145965540,3	K562	blood:
2	chr3:145961600..145965107-chr3:145968575..145970473,3	K562	blood:

Variant related genes	Relation type
ENSG00000114698	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10460850	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935609	0.92[ASN][1000 genomes]
rs12488776	0.91[ASN][1000 genomes]
rs12629875	0.92[ASN][1000 genomes]
rs13079270	0.93[ASN][1000 genomes]
rs13086396	0.92[ASN][1000 genomes]
rs13086427	0.85[ASN][1000 genomes]
rs1398527	0.87[ASN][1000 genomes]
rs1512894	0.93[ASN][1000 genomes]
rs1606265	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2036979	0.93[ASN][1000 genomes]
rs2175669	0.92[ASN][1000 genomes]
rs2867080	0.91[ASN][1000 genomes]
rs34773907	0.93[ASN][1000 genomes]
rs35187466	0.92[ASN][1000 genomes]
rs35499991	0.92[ASN][1000 genomes]
rs35616919	0.92[ASN][1000 genomes]
rs3804650	0.93[ASN][1000 genomes]
rs3804652	0.93[ASN][1000 genomes]
rs3804653	0.93[ASN][1000 genomes]
rs3828377	0.92[ASN][1000 genomes]
rs3828378	0.93[ASN][1000 genomes]
rs3828379	0.92[ASN][1000 genomes]
rs3920230	0.92[ASN][1000 genomes]
rs61207913	0.93[ASN][1000 genomes]
rs62272407	0.93[ASN][1000 genomes]
rs6808115	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3416330	chr3:145941029-146068457	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3452197	chr3:145950303-145974111	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	esv3333990	chr3:145950303-145982133	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv998388	chr3:145960954-146087749	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11926040	PLSCR4	cis	brain	BrainEAC

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145948000-145967800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:145953200-145968000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:145954600-145967800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:145956200-145964600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:145956800-145966600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:145958000-145965400	Weak transcription	Adipose Nuclei	Adipose
7	chr3:145958000-145966000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:145959400-145962800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:145959400-145966400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:145960000-145966400	Weak transcription	Ovary	ovary
11	chr3:145960200-145967800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:145960400-145963800	Weak transcription	HUVEC	blood vessel
13	chr3:145960400-145965400	Weak transcription	Fetal Stomach	stomach
14	chr3:145960400-145967800	Weak transcription	Fetal Intestine Large	intestine
15	chr3:145960800-145963800	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:145960800-145967800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:145960800-145967800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:145961800-145966200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:145962200-145962800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:145962200-145963000	Enhancers	NHDF-Ad	bronchial
21	chr3:145962200-145965800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:145962400-145962800	Strong transcription	Fetal Lung	lung
23	chr3:145962600-145962800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:145962600-145963000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:145962600-145966200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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