Variant report

Variant	rs3781620
Chromosome Location	chr11:47259264-47259265
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1051006	0.80[AMR][1000 genomes]
rs10838681	0.86[AFR][1000 genomes]
rs11039144	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039148	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039155	0.85[EUR][1000 genomes]
rs12574081	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1449626	0.80[AMR][1000 genomes]
rs16938581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242261	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242262	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279238	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306353	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2596397	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2596398	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2633080	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2633083	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2957873	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs326224	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3758670	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781619	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3824866	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4647725	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4647726	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4647737	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647741	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647754	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4647757	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4752972	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752973	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs4752977	0.81[AMR][1000 genomes]
rs59567949	0.80[AMR][1000 genomes]
rs7118396	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120158	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7395496	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7933246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947269	0.83[AMR][1000 genomes]
rs830083	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830084	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3781620	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs3781620	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs3781620	ACP2	cis	Thyroid	GTEx

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	chr11:47254800-47259400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr11:47254800-47259400	Weak transcription	Esophagus	oesophagus
22	chr11:47254800-47261000	Weak transcription	Ovary	ovary
23	chr11:47255400-47262000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr11:47255400-47269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:47255600-47264600	Strong transcription	HepG2	liver
26	chr11:47255600-47268800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:47255800-47267600	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr11:47256000-47260200	Weak transcription	Brain Substantia Nigra	brain
29	chr11:47256000-47260600	Weak transcription	Fetal Kidney	kidney
30	chr11:47256000-47268000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:47256200-47260400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:47256200-47260800	Strong transcription	Fetal Intestine Small	intestine
33	chr11:47256200-47267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:47256400-47259400	Weak transcription	Brain Anterior Caudate	brain
35	chr11:47256400-47259600	Weak transcription	Right Atrium	heart
36	chr11:47256400-47260600	Weak transcription	Brain Angular Gyrus	brain
37	chr11:47256400-47261000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:47256400-47267800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:47256600-47259400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr11:47256600-47259400	Weak transcription	Right Ventricle	heart
41	chr11:47256600-47259400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:47256600-47260000	Weak transcription	Brain Hippocampus Middle	brain
43	chr11:47256600-47261000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr11:47256800-47259400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:47256800-47259400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr11:47256800-47260800	Weak transcription	Stomach Mucosa	stomach
47	chr11:47256800-47268800	Strong transcription	Fetal Thymus	thymus
48	chr11:47257000-47259400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:47257000-47259400	Weak transcription	Adipose Nuclei	Adipose
50	chr11:47257000-47259400	Weak transcription	Duodenum Mucosa	Duodenum

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