Variant report

Variant	rs7109203
Chromosome Location	chr11:47265543-47265544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr11:47264664-47265660	MCF-7	breast:	n/a	n/a
2	FOXA2	chr11:47264781-47265560	A549	lung:	n/a	n/a
3	POLR2A	chr11:47258677-47266398	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47236414..47239398-chr11:47265054..47267561,5	K562	blood:
2	chr11:47205996..47209414-chr11:47263017..47267262,4	MCF-7	breast:
3	chr11:47205951..47209206-chr11:47263141..47266160,3	MCF-7	breast:
4	chr11:47264797..47267629-chr11:47289343..47292246,3	K562	blood:
5	chr11:47263774..47268457-chr11:47268937..47272422,6	MCF-7	breast:
6	chr11:47263865..47272320-chr11:47288426..47294726,14	MCF-7	breast:
7	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
8	chr11:47210760..47211699-chr11:47264854..47265597,2	MCF-7	breast:
9	chr11:47236332..47238351-chr11:47265199..47266819,2	MCF-7	breast:
10	chr11:47264727..47266306-chr11:47280070..47281666,2	K562	blood:
11	chr11:47263878..47266092-chr11:47289998..47293259,3	K562	blood:
12	chr11:47236127..47238090-chr11:47263739..47266462,2	MCF-7	breast:

No data

Variant related genes	Relation type
NR1H3	TF binding region
ENSG00000256746	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000134575	Chromatin interaction

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

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

rs_ID	r²[population]
rs10501321	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1055510	0.81[EUR][1000 genomes]
rs10742799	0.81[EUR][1000 genomes]
rs10838681	0.86[AMR][1000 genomes]
rs10838684	0.84[EUR][1000 genomes]
rs10838690	0.80[EUR][1000 genomes]
rs11039156	0.80[EUR][1000 genomes]
rs11039166	0.80[EUR][1000 genomes]
rs12575456	0.80[EUR][1000 genomes]
rs1375688	0.80[EUR][1000 genomes]
rs1449627	0.81[EUR][1000 genomes]
rs2013867	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2167079	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279239	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs326214	0.81[EUR][1000 genomes]
rs326222	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35879051	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3758669	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3758672	0.82[EUR][1000 genomes]
rs3758673	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3781621	0.80[EUR][1000 genomes]
rs3816725	0.81[EUR][1000 genomes]
rs3847502	0.80[EUR][1000 genomes]
rs4752822	0.87[EUR][1000 genomes]
rs4752824	0.80[EUR][1000 genomes]
rs4752980	0.80[EUR][1000 genomes]
rs59663860	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61896050	0.80[EUR][1000 genomes]
rs6485746	0.80[EUR][1000 genomes]
rs7120118	0.86[EUR][1000 genomes]
rs7120957	0.80[EUR][1000 genomes]
rs7124955	0.80[EUR][1000 genomes]
rs7127907	0.80[EUR][1000 genomes]
rs7129661	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7395581	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7940809	0.80[EUR][1000 genomes]
rs830085	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs901746	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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
rs7109203	ACP2	cis	Thyroid	GTEx
rs7109203	PACSIN3	cis	Esophagus Mucosa	GTEx
rs7109203	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr11:47240200-47266600	Weak transcription	Fetal Brain Male	brain
3	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:47243600-47269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:47246600-47267800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:47247400-47267600	Strong transcription	Thymus	Thymus
7	chr11:47254600-47267800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr11:47255400-47269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:47255600-47268800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:47255800-47267600	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr11:47256000-47268000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:47256200-47267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr11:47256400-47267800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr11:47256800-47268800	Strong transcription	Fetal Thymus	thymus
15	chr11:47257800-47267800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:47257800-47268000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:47258000-47269000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:47258200-47267600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:47258400-47266400	Strong transcription	Fetal Intestine Large	intestine
20	chr11:47258400-47267800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:47258400-47268400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:47258600-47267800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:47258600-47267800	Strong transcription	Rectal Smooth Muscle	rectum
24	chr11:47258600-47268800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:47258800-47267400	Strong transcription	Colon Smooth Muscle	Colon
26	chr11:47258800-47268000	Strong transcription	NHEK	skin
27	chr11:47259000-47268200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr11:47259000-47268800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:47259000-47269000	Strong transcription	Fetal Stomach	stomach
30	chr11:47259200-47268000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:47259400-47265600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:47259400-47266400	Strong transcription	Spleen	Spleen
33	chr11:47259400-47267400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr11:47259400-47267600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr11:47259400-47267600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:47259400-47267600	Strong transcription	Fetal Lung	lung
37	chr11:47259400-47267600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr11:47259400-47267800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr11:47259400-47267800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:47259400-47267800	Strong transcription	Primary T cells from cord blood	blood
41	chr11:47259400-47267800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr11:47259400-47267800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr11:47259400-47267800	Strong transcription	Gastric	stomach
44	chr11:47259400-47268000	Strong transcription	Brain Anterior Caudate	brain
45	chr11:47259400-47268000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr11:47259400-47268800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr11:47259400-47268800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr11:47259400-47269000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr11:47259400-47269000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:47259600-47267000	Strong transcription	Brain Germinal Matrix	brain

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