Variant report

Variant	rs11666282
Chromosome Location	chr19:35807845-35807846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr19:35807383-35807862	HepG2	liver:	n/a	n/a
2	FOXA1	chr19:35807398-35807976	HepG2	liver:	n/a	n/a
3	HNF4G	chr19:35807412-35807850	HepG2	liver:	n/a	n/a
4	FOXA1	chr19:35807357-35808030	HepG2	liver:	n/a	n/a
5	FOXA1	chr19:35807369-35807911	HepG2	liver:	n/a	n/a
6	EP300	chr19:35807437-35807908	HepG2	liver:	n/a	n/a
7	SP1	chr19:35807314-35807926	HepG2	liver:	n/a	n/a
8	MAX	chr19:35807313-35807884	HepG2	liver:	n/a	n/a
9	EP300	chr19:35807319-35807927	HepG2	liver:	n/a	n/a
10	EP300	chr19:35807488-35807849	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:35807544-35808119	K562	blood:	n/a	n/a
12	FOXA1	chr19:35807423-35807983	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35738973..35741505-chr19:35806828..35808599,2	MCF-7	breast:
2	chr19:35740175..35741891-chr19:35807694..35809845,2	MCF-7	breast:
3	chr19:35807787..35809317-chr19:35810235..35812842,2	K562	blood:
4	chr19:35755149..35764508-chr19:35799437..35813142,44	MCF-7	breast:
5	chr19:35757351..35762248-chr19:35804679..35808319,5	MCF-7	breast:
6	chr19:35801834..35808584-chr19:35810190..35813576,7	MCF-7	breast:

No data

Variant related genes	Relation type
CD22	TF binding region
ENSG00000012124	Chromatin interaction
ENSG00000105699	Chromatin interaction
ENSG00000105698	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11670792	0.94[CEU][hapmap]
rs11673522	1.00[CEU][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12461927	0.94[CEU][hapmap]
rs12463142	0.94[CEU][hapmap]
rs17637981	0.89[CEU][hapmap]
rs17705279	0.84[CEU][hapmap]
rs1858852	0.96[EUR][1000 genomes]
rs720308	0.94[CEU][hapmap]
rs720309	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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 miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong 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	59 gene(s)	inside rSNPs	diseases
8	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	esv1006379	chr19:35798572-35810821	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	n/a
10	nsv978807	chr19:35806669-35810074	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11666282	LGALS13	cis	cerebellum	SCAN
rs11666282	EGLN2	cis	cerebellum	SCAN
rs11666282	MAP3K10	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35774800-35809600	Weak transcription	Right Atrium	heart
2	chr19:35794400-35810000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:35797800-35809600	Weak transcription	Brain Angular Gyrus	brain
4	chr19:35798200-35811400	Weak transcription	Liver	Liver
5	chr19:35801000-35809400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:35803000-35808600	Weak transcription	Fetal Thymus	thymus
7	chr19:35803200-35808200	Weak transcription	Brain Anterior Caudate	brain
8	chr19:35803200-35808400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:35803200-35809600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:35803200-35809600	Weak transcription	Fetal Lung	lung
11	chr19:35803400-35809800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:35803400-35809800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:35804200-35809800	Weak transcription	Fetal Kidney	kidney
14	chr19:35804200-35811000	Enhancers	Primary B cells from peripheral blood	blood
15	chr19:35804600-35809400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:35804600-35809800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:35804800-35808000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:35804800-35808800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:35805000-35808200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:35805000-35808400	Weak transcription	Spleen	Spleen
21	chr19:35805000-35809200	Weak transcription	NHEK	skin
22	chr19:35805000-35809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:35805200-35809400	Weak transcription	HMEC	breast
24	chr19:35805200-35809600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:35805400-35808000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:35805400-35808400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr19:35805600-35811400	Enhancers	K562	blood
28	chr19:35806600-35808000	Flanking Active TSS	HepG2	liver
29	chr19:35806600-35809400	Enhancers	Hela-S3	cervix
30	chr19:35806800-35809400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr19:35806800-35810600	Enhancers	Primary B cells from cord blood	blood
32	chr19:35807000-35808000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:35807000-35809600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:35807200-35808000	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:35807200-35808400	Weak transcription	Ovary	ovary
36	chr19:35807400-35808000	Enhancers	GM12878-XiMat	blood
37	chr19:35807400-35808400	Enhancers	Duodenum Mucosa	Duodenum
38	chr19:35807400-35808400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr19:35807600-35808600	Genic enhancers	Brain Substantia Nigra	brain
40	chr19:35807800-35808600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr19:35807800-35812000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr19:35807800-35815800	Enhancers	Primary monocytes fromperipheralblood	blood

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