Variant report

Variant	rs3824866
Chromosome Location	chr11:47258853-47258854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47254323..47256222-chr11:47256983..47259410,2	MCF-7	breast:
2	chr11:47255922..47259235-chr11:47289768..47291804,3	MCF-7	breast:
3	chr11:47234544..47240299-chr11:47253173..47262641,20	MCF-7	breast:
4	chr11:47256660..47260798-chr11:47290143..47292249,4	K562	blood:
5	chr11:47257344..47261784-chr11:47428504..47430961,3	K562	blood:
6	chr11:47256660..47261423-chr11:47290143..47292492,5	K562	blood:
7	chr11:47257788..47261523-chr11:47268362..47272495,6	MCF-7	breast:
8	chr11:47234810..47237015-chr11:47256383..47258909,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255197	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000134575	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1051006	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs10769253	0.80[CEU][hapmap]
rs10838663	1.00[CEU][hapmap]
rs10838686	0.80[CEU][hapmap];0.83[YRI][hapmap]
rs10838689	0.80[CEU][hapmap]
rs11039144	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039148	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039155	0.85[EUR][1000 genomes]
rs12574081	0.87[EUR][1000 genomes]
rs12574410	1.00[CEU][hapmap]
rs1449626	0.82[AMR][1000 genomes]
rs16938581	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279238	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2290146	0.82[CEU][hapmap]
rs2290148	0.80[CEU][hapmap]
rs2306353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2596397	0.87[AMR][1000 genomes]
rs2596398	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633080	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2633083	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957873	0.82[CHB][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes]
rs326224	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3729802	0.85[CEU][hapmap];0.90[YRI][hapmap]
rs3758670	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781619	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781620	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4647725	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4647726	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647737	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647741	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647754	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647757	0.93[AMR][1000 genomes]
rs4752965	1.00[CEU][hapmap]
rs4752972	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752973	0.86[CHB][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes]
rs4752977	0.80[CEU][hapmap];0.83[YRI][hapmap]
rs4752983	0.80[CEU][hapmap];0.96[YRI][hapmap]
rs59567949	0.82[AMR][1000 genomes]
rs7118396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7120158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7395496	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs753992	0.80[CEU][hapmap]
rs7933246	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7947269	0.82[AMR][1000 genomes]
rs830083	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs830084	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3824866	ACP2	cis	Thyroid	GTEx
rs3824866	ACP2	cis	multi-tissue	Pritchard
rs3824866	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs3824866	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47238600-47259600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:47238600-47261000	Weak transcription	Small Intestine	intestine
4	chr11:47240000-47260200	Weak transcription	Fetal Brain Female	brain
5	chr11:47240200-47266600	Weak transcription	Fetal Brain Male	brain
6	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:47242600-47259600	Weak transcription	Brain Germinal Matrix	brain
8	chr11:47242600-47260200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:47243600-47269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:47246600-47267800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:47247400-47267600	Strong transcription	Thymus	Thymus
12	chr11:47248200-47259400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:47248200-47265200	Strong transcription	GM12878-XiMat	blood
14	chr11:47248600-47260800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:47249400-47259400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:47251200-47259400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:47252000-47259600	Weak transcription	Fetal Muscle Leg	muscle
18	chr11:47254000-47264600	Strong transcription	Dnd41	blood
19	chr11:47254600-47267800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:47254800-47259200	Weak transcription	Lung	lung
21	chr11:47254800-47259400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr11:47254800-47259400	Weak transcription	Esophagus	oesophagus
23	chr11:47254800-47261000	Weak transcription	Ovary	ovary
24	chr11:47255400-47262000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr11:47255400-47269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:47255600-47264600	Strong transcription	HepG2	liver
27	chr11:47255600-47268800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:47255800-47267600	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr11:47256000-47260200	Weak transcription	Brain Substantia Nigra	brain
30	chr11:47256000-47260600	Weak transcription	Fetal Kidney	kidney
31	chr11:47256000-47268000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:47256200-47260400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:47256200-47260800	Strong transcription	Fetal Intestine Small	intestine
34	chr11:47256200-47267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:47256400-47259400	Weak transcription	Brain Anterior Caudate	brain
36	chr11:47256400-47259600	Weak transcription	Right Atrium	heart
37	chr11:47256400-47260600	Weak transcription	Brain Angular Gyrus	brain
38	chr11:47256400-47261000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:47256400-47267800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr11:47256600-47259400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr11:47256600-47259400	Weak transcription	Right Ventricle	heart
42	chr11:47256600-47259400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:47256600-47260000	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:47256600-47261000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr11:47256800-47259400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:47256800-47259400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr11:47256800-47260800	Weak transcription	Stomach Mucosa	stomach
48	chr11:47256800-47268800	Strong transcription	Fetal Thymus	thymus
49	chr11:47257000-47259000	Genic enhancers	HUVEC	blood vessel
50	chr11:47257000-47259400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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