Variant report

Variant	rs11046099
Chromosome Location	chr12:21672296-21672297
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21671832..21674785-chr12:21687913..21690095,2	K562	blood:
2	chr12:21654473..21659052-chr12:21670057..21674835,6	K562	blood:

Variant related genes	Relation type
ENSG00000004700	Chromatin interaction
ENSG00000111711	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10770819	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs10841839	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10841840	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11046089	0.81[EUR][1000 genomes]
rs11046098	0.94[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11046100	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12423412	0.88[EUR][1000 genomes]
rs12829508	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12833589	0.84[EUR][1000 genomes]
rs4762834	0.81[EUR][1000 genomes]
rs61926331	0.84[EUR][1000 genomes]
rs61926332	0.84[EUR][1000 genomes]

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	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer 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 target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv528556	chr12:21664879-21680363	Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv557743	chr12:21670410-21688900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11046099	PYROXD1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21655400-21674800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:21656000-21672800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:21656000-21674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:21656000-21674600	Weak transcription	Fetal Kidney	kidney
5	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
6	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
7	chr12:21656800-21680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:21657400-21680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:21657600-21675000	Weak transcription	Small Intestine	intestine
10	chr12:21657600-21675400	Weak transcription	Fetal Brain Male	brain
11	chr12:21657600-21679800	Weak transcription	Pancreas	Pancrea
12	chr12:21657600-21680000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:21657600-21680400	Weak transcription	Gastric	stomach
14	chr12:21660200-21672600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:21660600-21672600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:21660800-21672400	Strong transcription	Liver	Liver
17	chr12:21661400-21677200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:21662200-21672400	Strong transcription	HSMM	muscle
19	chr12:21664800-21672400	Strong transcription	NH-A	brain
20	chr12:21665800-21672400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:21666000-21680200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:21666800-21672800	Weak transcription	NHEK	skin
23	chr12:21666800-21675800	Weak transcription	HepG2	liver
24	chr12:21666800-21676800	Weak transcription	Fetal Brain Female	brain
25	chr12:21666800-21679800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:21666800-21680000	Weak transcription	Psoas Muscle	Psoas
27	chr12:21666800-21680200	Weak transcription	Colonic Mucosa	Colon
28	chr12:21666800-21680400	Weak transcription	Spleen	Spleen
29	chr12:21667000-21674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:21667000-21674400	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:21667000-21675000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:21667000-21680200	Weak transcription	Left Ventricle	heart
33	chr12:21667000-21680200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:21667000-21680200	Weak transcription	HSMMtube	muscle
35	chr12:21667200-21672600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:21667200-21678000	Weak transcription	Lung	lung
37	chr12:21667200-21680000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:21667200-21680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:21667200-21680000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:21667400-21672400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:21667400-21672800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr12:21667400-21673000	Weak transcription	Fetal Intestine Large	intestine
43	chr12:21667600-21680000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr12:21667600-21680200	Weak transcription	NHLF	lung
45	chr12:21667800-21673400	Weak transcription	Colon Smooth Muscle	Colon
46	chr12:21669200-21672800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:21669200-21675400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:21669200-21680000	Weak transcription	HMEC	breast
49	chr12:21669400-21673000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:21669400-21675800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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