Variant report

Variant	rs2444240
Chromosome Location	chr11:120040442-120040443
allele	A/C
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:120038992..120040633-chr11:120083752..120086483,2	K562	blood:
2	chr11:120036264..120041871-chr11:120106231..120109757,9	K562	blood:
3	chr11:120039493..120041713-chr11:120171400..120173344,2	MCF-7	breast:
4	chr11:120037531..120041521-chr11:120105416..120108760,8	K562	blood:
5	chr11:120040154..120042795-chr11:120100030..120102523,3	K562	blood:
6	chr11:120040035..120042877-chr11:120088247..120091000,2	K562	blood:
7	chr11:119990371..119993698-chr11:120037887..120041016,6	MCF-7	breast:
8	chr11:120038506..120040920-chr11:120082703..120085252,3	K562	blood:
9	chr11:120040105..120041638-chr11:120170388..120172497,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184232	Chromatin interaction
ENSG00000137709	Chromatin interaction
ENSG00000137699	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs470370	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs470373	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs470645	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs470876	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs470941	0.87[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs471001	0.86[ASN][1000 genomes]
rs488672	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4936509	0.92[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4938790	0.91[ASN][1000 genomes]
rs521556	0.96[ASN][1000 genomes]
rs528147	0.93[ASN][1000 genomes]
rs529657	0.96[ASN][1000 genomes]
rs529681	0.93[ASN][1000 genomes]
rs531260	0.99[ASN][1000 genomes]
rs533636	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs550164	0.87[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs561498	0.94[JPT][hapmap]
rs566935	0.81[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs573211	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs605374	0.87[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs626225	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs670855	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs896691	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Corneal curvature	22969067	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2444240	RNF214	cis	cerebellum	SCAN
rs2444240	SORL1	cis	cerebellum	SCAN
rs2444240	UBE4A	cis	parietal	SCAN
rs2444240	DPAGT1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120039200-120040800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:120039200-120040800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:120039200-120040800	Bivalent/Poised TSS	Fetal Brain Female	brain
4	chr11:120039200-120040800	Enhancers	Spleen	Spleen
5	chr11:120039200-120041000	Bivalent Enhancer	Fetal Heart	heart
6	chr11:120039200-120041200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr11:120039400-120040600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:120039400-120040600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:120039400-120040600	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr11:120039400-120040600	Flanking Active TSS	HMEC	breast
11	chr11:120039400-120040600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr11:120039400-120040800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr11:120039400-120041000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:120039600-120040600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr11:120039600-120041000	Active TSS	Brain Cingulate Gyrus	brain
16	chr11:120039800-120040600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr11:120039800-120040800	Active TSS	Brain Substantia Nigra	brain
18	chr11:120039800-120041200	Bivalent Enhancer	Fetal Brain Male	brain
19	chr11:120040000-120040600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:120040000-120040600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
21	chr11:120040000-120040600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:120040000-120040600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
23	chr11:120040000-120040600	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr11:120040000-120040800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:120040000-120040800	Flanking Active TSS	Liver	Liver
26	chr11:120040000-120040800	Flanking Active TSS	Esophagus	oesophagus
27	chr11:120040000-120040800	Enhancers	Lung	lung
28	chr11:120040000-120040800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
29	chr11:120040200-120040600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
30	chr11:120040200-120040600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
31	chr11:120040200-120040600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
32	chr11:120040200-120040600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:120040200-120040600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:120040200-120040600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
35	chr11:120040200-120040600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
36	chr11:120040200-120040600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
37	chr11:120040200-120040600	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
38	chr11:120040200-120040600	Flanking Active TSS	HepG2	liver
39	chr11:120040200-120040800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:120040200-120040800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:120040200-120040800	Enhancers	Pancreas	Pancrea
42	chr11:120040200-120041000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr11:120040200-120041000	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr11:120040200-120041000	Bivalent Enhancer	Left Ventricle	heart
45	chr11:120040200-120041400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:120040400-120040600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:120040400-120040600	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:120040400-120040600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr11:120040400-120040600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
50	chr11:120040400-120040600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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