Variant report

Variant	rs747782
Chromosome Location	chr11:47940925-47940926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1017875	1.00[CEU][hapmap]
rs1681630	0.93[GIH][hapmap];0.88[JPT][hapmap]
rs2305983	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap]
rs4752805	0.93[CEU][hapmap]
rs59185955	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485774	0.86[CEU][hapmap];0.93[TSI][hapmap]
rs6485788	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap]
rs7123436	1.00[CEU][hapmap]
rs7130876	0.93[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs7927682	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7942031	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap]
rs7944735	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv825876	chr11:47939505-47941020	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Intraocular pressure	25173106	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs747782	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs747782	OR4C3	cis	parietal	SCAN
rs747782	LOC441601	cis	cerebellum	SCAN
rs747782	RAPSN	cis	cerebellum	SCAN
rs747782	ATG13	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47925600-47943200	Enhancers	Placenta	Placenta
2	chr11:47927200-47942800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:47934000-47946600	Enhancers	Primary B cells from cord blood	blood
4	chr11:47934400-47947200	Enhancers	Primary B cells from peripheral blood	blood
5	chr11:47935400-47944600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:47935600-47941200	Enhancers	HUVEC	blood vessel
7	chr11:47936400-47941200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr11:47936600-47941800	Enhancers	Fetal Thymus	thymus
9	chr11:47936800-47941000	Enhancers	Spleen	Spleen
10	chr11:47937000-47941200	Enhancers	Pancreas	Pancrea
11	chr11:47937000-47941400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:47937200-47941200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:47937400-47942000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:47937400-47949800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:47937600-47941200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:47937800-47941400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:47938400-47945600	Weak transcription	Left Ventricle	heart
18	chr11:47938800-47941200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:47938800-47943200	Enhancers	Dnd41	blood
20	chr11:47939000-47941000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr11:47939000-47941400	Flanking Active TSS	Hela-S3	cervix
22	chr11:47939000-47943200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:47939000-47943600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:47939200-47943000	Enhancers	Primary hematopoietic stem cells	blood
25	chr11:47939200-47943000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr11:47939200-47944600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr11:47939400-47941000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:47939400-47941200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:47939400-47941200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:47939400-47943200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr11:47939400-47943800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr11:47939600-47941000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:47939600-47941200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:47939600-47941200	Enhancers	NH-A	brain
35	chr11:47939600-47941400	Enhancers	Osteobl	bone
36	chr11:47939600-47941600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:47939600-47941600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:47939600-47941600	Enhancers	NHDF-Ad	bronchial
39	chr11:47939600-47941800	Enhancers	Primary T cells from cord blood	blood
40	chr11:47939600-47942000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr11:47939600-47943200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:47939600-47943200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr11:47939600-47944600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr11:47939600-47946600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:47939800-47941200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr11:47939800-47945200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:47940000-47941000	Enhancers	Duodenum Mucosa	Duodenum
48	chr11:47940000-47941000	Enhancers	Fetal Muscle Trunk	muscle
49	chr11:47940000-47941200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:47940000-47941200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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