Variant report

Variant	rs3729802
Chromosome Location	chr11:47354068-47354069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47346954..47348985-chr11:47352662..47354542,2	MCF-7	breast:
2	chr11:47290102..47294520-chr11:47352678..47355861,4	K562	blood:
3	chr11:47291226..47293092-chr11:47352052..47354178,2	K562	blood:
4	chr11:47347273..47351481-chr11:47353649..47359054,5	K562	blood:
5	chr11:47350500..47353711-chr11:47353800..47358007,4	MCF-7	breast:
6	chr11:47353935..47356696-chr11:47429697..47432072,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256746	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000255197	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1044269	0.82[CEU][hapmap]
rs1051006	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10769253	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10769254	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10769255	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838663	0.85[CEU][hapmap]
rs10838685	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838686	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838687	0.86[AMR][1000 genomes]
rs10838689	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039155	0.87[EUR][1000 genomes]
rs11039189	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11493249	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11530166	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11821917	0.85[CEU][hapmap]
rs11824864	0.85[CEU][hapmap]
rs11828339	0.85[CEU][hapmap]
rs12222581	0.82[AMR][1000 genomes]
rs12574081	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12574410	0.85[CEU][hapmap]
rs1449626	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17198158	0.85[CEU][hapmap]
rs17790804	0.85[CEU][hapmap]
rs2242261	0.85[CEU][hapmap];0.80[YRI][hapmap]
rs2242262	0.85[CEU][hapmap]
rs2242511	0.85[CEU][hapmap]
rs2254240	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279238	0.85[CEU][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2290146	0.86[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290148	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306353	0.85[CEU][hapmap]
rs2633080	0.82[CEU][hapmap]
rs3729804	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3729805	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781619	0.85[CEU][hapmap];0.85[YRI][hapmap]
rs3824866	0.85[CEU][hapmap];0.90[YRI][hapmap]
rs3847503	0.85[CEU][hapmap]
rs4752839	0.85[CEU][hapmap]
rs4752965	0.85[CEU][hapmap]
rs4752977	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752978	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752979	0.89[AMR][1000 genomes]
rs4752983	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58023804	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59567949	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6485751	0.89[AMR][1000 genomes]
rs7118396	0.85[CEU][hapmap];0.94[YRI][hapmap]
rs7124958	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7395496	0.85[CEU][hapmap]
rs753812	1.00[CEU][hapmap]
rs753992	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs753993	0.84[AMR][1000 genomes]
rs7928073	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs830084	0.82[CEU][hapmap]
rs9666924	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv554209	chr11:47353498-47364127	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3729802	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs3729802	DDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47294600-47355200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr11:47324200-47354600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr11:47338800-47356200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:47343200-47370600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:47347800-47354800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:47348000-47358200	Weak transcription	K562	blood
7	chr11:47348600-47355000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:47350400-47356800	Genic enhancers	Right Ventricle	heart
9	chr11:47350800-47354400	Genic enhancers	Left Ventricle	heart
10	chr11:47350800-47357400	Weak transcription	HepG2	liver
11	chr11:47351000-47355800	Enhancers	Fetal Heart	heart
12	chr11:47351200-47354200	Weak transcription	Osteobl	bone
13	chr11:47351200-47354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:47351400-47354800	Weak transcription	Brain Angular Gyrus	brain
15	chr11:47351400-47358800	Weak transcription	Aorta	Aorta
16	chr11:47351400-47375600	Weak transcription	Primary B cells from cord blood	blood
17	chr11:47351600-47358400	Weak transcription	A549	lung
18	chr11:47351600-47358600	Weak transcription	Hela-S3	cervix
19	chr11:47352000-47354200	Weak transcription	Primary T cells from cord blood	blood
20	chr11:47352000-47354200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr11:47352000-47354200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr11:47352200-47354600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:47352200-47355400	Weak transcription	Fetal Brain Female	brain
24	chr11:47352400-47354200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:47352400-47354200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:47352400-47354200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:47352400-47354200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:47352400-47354200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:47352400-47354200	Enhancers	Colonic Mucosa	Colon
30	chr11:47352400-47354200	Weak transcription	Ovary	ovary
31	chr11:47352400-47354400	Weak transcription	HSMMtube	muscle
32	chr11:47352400-47354600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr11:47352400-47354800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr11:47352400-47355000	Weak transcription	Brain Substantia Nigra	brain
35	chr11:47352400-47355200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:47352400-47355600	Weak transcription	Thymus	Thymus
37	chr11:47352400-47355800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr11:47352400-47356000	Strong transcription	Spleen	Spleen
39	chr11:47352400-47356200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:47352400-47364000	Weak transcription	Lung	lung
41	chr11:47352600-47354200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr11:47352600-47354200	Weak transcription	Liver	Liver
43	chr11:47352600-47354400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:47352600-47354400	Weak transcription	GM12878-XiMat	blood
45	chr11:47352600-47354600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:47352600-47354800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:47352600-47355200	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:47352600-47356000	Weak transcription	NHLF	lung
49	chr11:47352600-47363200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:47352600-47366000	Weak transcription	Brain Germinal Matrix	brain

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