Variant report

Variant	rs12792498
Chromosome Location	chr11:5663575-5663576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:5469844-5475173..11:5661051-5666977	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000187918	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11038508	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11038521	0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7950311	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers 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 target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12792498	OR51I2	cis	cerebellum	SCAN
rs12792498	SYT9	cis	parietal	SCAN
rs12792498	EIF3F	cis	cerebellum	SCAN
rs12792498	CCKBR	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5647000-5666800	Weak transcription	Fetal Brain Male	brain
2	chr11:5647000-5698800	Weak transcription	Colonic Mucosa	Colon
3	chr11:5647400-5664600	Weak transcription	Fetal Kidney	kidney
4	chr11:5647400-5667200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:5647400-5669400	Weak transcription	Right Ventricle	heart
6	chr11:5647400-5675600	Weak transcription	Pancreas	Pancrea
7	chr11:5647400-5689400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:5647600-5665600	Weak transcription	Stomach Mucosa	stomach
9	chr11:5647600-5665800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:5647600-5668000	Weak transcription	A549	lung
11	chr11:5647800-5690600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:5649200-5695600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:5653200-5665400	Strong transcription	Primary T cells from cord blood	blood
14	chr11:5653600-5665800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:5654000-5665200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:5654000-5666000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:5654000-5666000	Strong transcription	Primary B cells from cord blood	blood
18	chr11:5654000-5666400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:5654400-5666200	Strong transcription	Liver	Liver
20	chr11:5654400-5666200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:5654400-5666400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr11:5654600-5665600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:5654600-5666400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:5655800-5674200	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:5656200-5664600	Weak transcription	Spleen	Spleen
26	chr11:5656200-5667000	Weak transcription	NHLF	lung
27	chr11:5656200-5675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:5656400-5663600	Weak transcription	Fetal Thymus	thymus
29	chr11:5656400-5663600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:5656400-5667000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:5656400-5684600	Weak transcription	Osteobl	bone
32	chr11:5656400-5688800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr11:5656800-5664600	Weak transcription	Fetal Intestine Small	intestine
34	chr11:5657400-5668400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr11:5658000-5664600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:5659800-5665400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr11:5660000-5663600	Weak transcription	Fetal Lung	lung
38	chr11:5660200-5664400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:5660800-5664600	Weak transcription	Fetal Heart	heart
40	chr11:5661000-5665400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:5661200-5666200	Strong transcription	Adipose Nuclei	Adipose
42	chr11:5661600-5667800	Weak transcription	Brain Substantia Nigra	brain
43	chr11:5662000-5665600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:5662000-5667000	Strong transcription	Placenta	Placenta
45	chr11:5662200-5665400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr11:5662400-5664000	Strong transcription	Small Intestine	intestine
47	chr11:5662400-5664200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr11:5662400-5665000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr11:5662400-5665400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr11:5662400-5665400	Strong transcription	Rectal Mucosa Donor 31	rectum

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