Variant report

Variant	rs4647754
Chromosome Location	chr11:47257340-47257341
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 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	chr11:47251551..47253221-chr11:47255749..47257374,2	K562	blood:
4	chr11:47207072..47208935-chr11:47255110..47257481,3	MCF-7	breast:
5	chr11:47234544..47240299-chr11:47253173..47262641,20	MCF-7	breast:
6	chr11:47256660..47260798-chr11:47290143..47292249,4	K562	blood:
7	chr11:47249459..47253221-chr11:47254419..47257374,3	K562	blood:
8	chr11:47209362..47211566-chr11:47254961..47257621,2	MCF-7	breast:
9	chr11:47256660..47261423-chr11:47290143..47292492,5	K562	blood:
10	chr11:47254714..47257684-chr11:47290232..47292284,2	MCF-7	breast:
11	chr11:47255507..47257746-chr11:47267199..47270401,3	MCF-7	breast:
12	chr11:47234810..47237015-chr11:47256383..47258909,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000025434	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000134574	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1051006	0.82[AMR][1000 genomes]
rs11039144	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039148	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]
rs1449626	0.82[AMR][1000 genomes]
rs16938581	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242261	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242262	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279238	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2306353	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	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2633083	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2957873	0.87[AMR][1000 genomes]
rs326224	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3758670	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781620	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3824866	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647725	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4647726	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647737	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647741	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647757	0.93[AMR][1000 genomes]
rs4752972	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752973	0.96[AMR][1000 genomes]
rs59567949	0.82[AMR][1000 genomes]
rs7118396	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7120158	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7395496	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7933246	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7947269	0.82[AMR][1000 genomes]
rs830083	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830084	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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
rs4647754	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs4647754	ACP2	cis	Thyroid	GTEx
rs4647754	DDB2	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	chr11:47242200-47258200	Weak transcription	Fetal Lung	lung
7	chr11:47242400-47257800	Weak transcription	K562	blood
8	chr11:47242400-47258000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:47242400-47258000	Weak transcription	Primary B cells from cord blood	blood
10	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:47242600-47259600	Weak transcription	Brain Germinal Matrix	brain
12	chr11:47242600-47260200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr11:47243600-47269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr11:47246600-47267800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:47247400-47267600	Strong transcription	Thymus	Thymus
16	chr11:47248200-47258600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:47248200-47259400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:47248200-47265200	Strong transcription	GM12878-XiMat	blood
19	chr11:47248600-47260800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:47249400-47259400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:47251200-47259400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:47252000-47259600	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:47253800-47258200	Strong transcription	Fetal Stomach	stomach
24	chr11:47254000-47264600	Strong transcription	Dnd41	blood
25	chr11:47254200-47258800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:47254600-47258200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:47254600-47267800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:47254800-47257400	Genic enhancers	HMEC	breast
29	chr11:47254800-47259200	Weak transcription	Lung	lung
30	chr11:47254800-47259400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr11:47254800-47259400	Weak transcription	Esophagus	oesophagus
32	chr11:47254800-47261000	Weak transcription	Ovary	ovary
33	chr11:47255400-47262000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr11:47255400-47269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr11:47255600-47257400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr11:47255600-47257400	Strong transcription	Placenta	Placenta
37	chr11:47255600-47258800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:47255600-47264600	Strong transcription	HepG2	liver
39	chr11:47255600-47268800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:47255800-47257600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:47255800-47267600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr11:47256000-47258000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr11:47256000-47260200	Weak transcription	Brain Substantia Nigra	brain
44	chr11:47256000-47260600	Weak transcription	Fetal Kidney	kidney
45	chr11:47256000-47268000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:47256200-47258400	Weak transcription	Fetal Intestine Large	intestine
47	chr11:47256200-47260400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr11:47256200-47260800	Strong transcription	Fetal Intestine Small	intestine
49	chr11:47256200-47267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr11:47256400-47257400	Enhancers	Primary T helper cells fromperipheralblood	blood

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