Variant report

Variant	rs2279239
Chromosome Location	chr11:47281780-47281781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:47278588-47281976	A549	lung:	n/a	chr11:47278969-47278982
2	HCFC1	chr11:47278486-47281950	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:47197631..47199665-chr11:47279516..47282212,2	K562	blood:
2	chr11:47206745..47208837-chr11:47280102..47282885,2	K562	blood:
3	chr11:47196892..47202921-chr11:47278417..47285951,9	MCF-7	breast:
4	chr11:47205835..47208468-chr11:47280225..47282817,2	MCF-7	breast:
5	chr11:47281216..47281858-chr11:47376450..47377036,2	MCF-7	breast:
6	chr11:47200760..47201391-chr11:47280819..47281923,3	MCF-7	breast:
7	chr11:47197941..47200223-chr11:47281634..47284173,2	K562	blood:
8	chr11:47279843..47284326-chr11:47288675..47293634,16	MCF-7	breast:
9	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
10	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
11	chr11:47277979..47283267-chr11:47289057..47293509,9	K562	blood:
12	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:

No data

Variant related genes	Relation type
NR1H3	TF binding region
ENSG00000025434	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000134575	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10501321	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1052373	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1055510	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10742799	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10742801	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10769252	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10838681	0.82[AMR][1000 genomes]
rs10838684	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838690	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10838691	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10838692	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10838693	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11039156	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039166	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11039167	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12575456	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1375688	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1449627	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2013867	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2167079	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2301216	0.82[AMR][1000 genomes]
rs326214	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs326222	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35879051	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3758669	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3758672	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3758673	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781621	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3781622	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3816725	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3847502	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4752822	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752824	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4752825	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4752980	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59663860	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61896050	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6485746	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7109147	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7109203	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7120118	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120957	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7124955	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7127907	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7129661	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7395581	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7940809	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs830085	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs901746	0.90[EUR][1000 genomes];0.84[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
rs2279239	PACSIN3	cis	Esophagus Mucosa	GTEx
rs2279239	ACP2	cis	Thyroid	GTEx
rs2279239	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47272400-47286400	Weak transcription	Dnd41	blood
2	chr11:47275800-47286800	Weak transcription	Primary T cells from cord blood	blood
3	chr11:47277000-47282000	Weak transcription	Spleen	Spleen
4	chr11:47278600-47282000	Flanking Active TSS	Hela-S3	cervix
5	chr11:47278800-47282000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:47278800-47282200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:47278800-47282200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr11:47279200-47288800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:47279400-47286800	Weak transcription	NHEK	skin
10	chr11:47279400-47289400	Weak transcription	Fetal Brain Female	brain
11	chr11:47279800-47287000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:47279800-47289800	Weak transcription	Esophagus	oesophagus
13	chr11:47280000-47282000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:47280000-47282800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:47280000-47289400	Weak transcription	Brain Angular Gyrus	brain
16	chr11:47280000-47289600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:47280000-47290000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:47280200-47282200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:47280200-47282200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr11:47280200-47282800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:47280200-47289400	Weak transcription	Pancreas	Pancrea
22	chr11:47280200-47289600	Weak transcription	Brain Substantia Nigra	brain
23	chr11:47280200-47289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:47280200-47289800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:47280200-47290600	Weak transcription	Ovary	ovary
26	chr11:47280200-47290800	Weak transcription	Aorta	Aorta
27	chr11:47280400-47282000	Enhancers	Colon Smooth Muscle	Colon
28	chr11:47280600-47289800	Weak transcription	Fetal Kidney	kidney
29	chr11:47280800-47282000	Enhancers	Gastric	stomach
30	chr11:47280800-47282200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:47281000-47281800	Enhancers	Fetal Intestine Large	intestine
32	chr11:47281000-47284800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:47281000-47285800	Weak transcription	Osteobl	bone
34	chr11:47281000-47286200	Weak transcription	NHDF-Ad	bronchial
35	chr11:47281000-47289800	Weak transcription	Fetal Brain Male	brain
36	chr11:47281000-47290800	Weak transcription	Small Intestine	intestine
37	chr11:47281200-47281800	Enhancers	Liver	Liver
38	chr11:47281200-47282000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:47281200-47282000	Genic enhancers	Fetal Intestine Small	intestine
40	chr11:47281200-47283600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:47281200-47285800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:47281200-47285800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr11:47281200-47286200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr11:47281200-47286800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:47281200-47289000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:47281200-47289200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:47281200-47289400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr11:47281200-47289400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:47281200-47289400	Weak transcription	Fetal Lung	lung
50	chr11:47281200-47290000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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