Variant report

Variant	rs3729804
Chromosome Location	chr11:47352862-47352863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47196984..47198613-chr11:47350804..47352943,2	MCF-7	breast:
2	chr11:47346954..47348985-chr11:47352662..47354542,2	MCF-7	breast:
3	chr11:47290102..47294520-chr11:47352678..47355861,4	K562	blood:
4	chr11:47291226..47293092-chr11:47352052..47354178,2	K562	blood:
5	chr11:47352757..47353542-chr11:47376561..47377283,2	MCF-7	breast:
6	chr11:47352349..47353915-chr11:47361681..47363878,2	MCF-7	breast:
7	chr11:47350500..47353711-chr11:47353800..47358007,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110514	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000149182	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1051006	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10769253	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10769254	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10769255	0.93[EUR][1000 genomes]
rs10838685	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10838686	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838687	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10838689	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039155	0.84[EUR][1000 genomes]
rs11039189	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11493249	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11530166	0.85[AMR][1000 genomes]
rs12222581	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12574081	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1449626	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2254240	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279238	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2290146	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290148	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305280	0.82[AFR][1000 genomes]
rs3729802	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3729805	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752977	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752978	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752979	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4752983	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58023804	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59567949	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6485751	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7124958	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs753992	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs753993	0.86[AMR][1000 genomes]
rs7928073	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3729804	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs3729804	ACP2	cis	Thyroid	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47294600-47355200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr11:47296000-47353600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:47324200-47354600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr11:47325400-47353000	Strong transcription	Fetal Intestine Small	intestine
5	chr11:47326000-47353600	Strong transcription	Fetal Stomach	stomach
6	chr11:47338800-47356200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:47339200-47353000	Weak transcription	NH-A	brain
8	chr11:47342200-47353200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:47342600-47353200	Strong transcription	Placenta	Placenta
10	chr11:47342800-47353000	Strong transcription	Fetal Intestine Large	intestine
11	chr11:47342800-47353600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:47343200-47370600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr11:47344800-47353000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:47345000-47353000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:47347800-47353400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:47347800-47353400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:47347800-47354000	Weak transcription	HSMM	muscle
18	chr11:47347800-47354800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:47348000-47358200	Weak transcription	K562	blood
20	chr11:47348600-47355000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:47349800-47354000	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr11:47350400-47353000	Genic enhancers	Fetal Muscle Leg	muscle
23	chr11:47350400-47353200	Genic enhancers	Adipose Nuclei	Adipose
24	chr11:47350400-47356800	Genic enhancers	Right Ventricle	heart
25	chr11:47350600-47353400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr11:47350800-47353000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr11:47350800-47353200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr11:47350800-47353200	Genic enhancers	Gastric	stomach
29	chr11:47350800-47354400	Genic enhancers	Left Ventricle	heart
30	chr11:47350800-47357400	Weak transcription	HepG2	liver
31	chr11:47351000-47354000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:47351000-47355800	Enhancers	Fetal Heart	heart
33	chr11:47351200-47353200	Strong transcription	NHEK	skin
34	chr11:47351200-47353800	Weak transcription	Fetal Lung	lung
35	chr11:47351200-47353800	Enhancers	Stomach Mucosa	stomach
36	chr11:47351200-47354200	Weak transcription	Osteobl	bone
37	chr11:47351200-47354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:47351400-47353000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr11:47351400-47353200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:47351400-47353200	Weak transcription	Small Intestine	intestine
41	chr11:47351400-47353400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr11:47351400-47354800	Weak transcription	Brain Angular Gyrus	brain
43	chr11:47351400-47358800	Weak transcription	Aorta	Aorta
44	chr11:47351400-47375600	Weak transcription	Primary B cells from cord blood	blood
45	chr11:47351600-47353200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr11:47351600-47353400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr11:47351600-47358400	Weak transcription	A549	lung
48	chr11:47351600-47358600	Weak transcription	Hela-S3	cervix
49	chr11:47351800-47353000	Weak transcription	Esophagus	oesophagus
50	chr11:47351800-47353400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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