Variant report

Variant	rs11927939
Chromosome Location	chr3:118926750-118926751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:118925125..118927073-chr3:118927779..118929469,2	MCF-7	breast:
2	chr3:118924439..118927161-chr3:118936255..118939127,2	MCF-7	breast:
3	chr3:118925359..118927166-chr3:118958232..118960425,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121578	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10511382	1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12634868	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13081519	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs16829477	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829479	0.85[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs3796356	0.96[EUR][1000 genomes]
rs3796357	0.85[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs4370022	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687840	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687980	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687981	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687982	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57258193	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58939003	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61162364	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438502	0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs6438506	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7426444	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs9840317	0.80[GIH][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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 target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription 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	15 gene(s)	inside rSNPs	diseases
4	nsv591362	chr3:118906442-118948155	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11927939	PLA1A	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118904600-118936400	Weak transcription	Gastric	stomach
2	chr3:118908400-118928200	Weak transcription	Fetal Stomach	stomach
3	chr3:118911800-118932600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:118915200-118928400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:118915200-118934800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:118920400-118930400	Weak transcription	Fetal Kidney	kidney
7	chr3:118921000-118928000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:118921400-118931200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:118922200-118927400	Weak transcription	HSMM	muscle
10	chr3:118922600-118929000	Weak transcription	Spleen	Spleen
11	chr3:118923000-118927600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:118923000-118929000	Weak transcription	Brain Germinal Matrix	brain
13	chr3:118923200-118927400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:118923400-118926800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:118923400-118927000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:118923400-118927400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr3:118923600-118930800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:118923800-118931600	Enhancers	Stomach Mucosa	stomach
19	chr3:118924200-118926800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr3:118924200-118927200	Enhancers	Fetal Thymus	thymus
21	chr3:118924200-118927800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:118924200-118931600	Weak transcription	NHDF-Ad	bronchial
23	chr3:118924400-118927600	Weak transcription	Aorta	Aorta
24	chr3:118924400-118928200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr3:118924400-118929200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:118924400-118929800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:118924400-118933200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:118924400-118959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:118924600-118926800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:118924600-118927200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:118924600-118927800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:118924600-118928000	Weak transcription	Ovary	ovary
33	chr3:118924600-118929000	Weak transcription	Colonic Mucosa	Colon
34	chr3:118924600-118930000	Weak transcription	Osteobl	bone
35	chr3:118924600-118930200	Weak transcription	Fetal Lung	lung
36	chr3:118924600-118945600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:118924800-118927200	Enhancers	NHEK	skin
38	chr3:118924800-118927400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:118924800-118928000	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:118924800-118928400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:118924800-118929400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:118924800-118931200	Weak transcription	Right Ventricle	heart
43	chr3:118925000-118926800	Enhancers	HMEC	breast
44	chr3:118925200-118926800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:118925200-118927000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:118925200-118927000	Enhancers	K562	blood
47	chr3:118925200-118927200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:118925400-118926800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr3:118925400-118926800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:118925400-118927000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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