Variant report

Variant	rs11183799
Chromosome Location	chr12:47604412-47604413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47598802..47603269-chr12:47603355..47607825,7	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMIGO2-1	chr12:47602203-47604544	ENSG00000247774
2	lnc-AMIGO2-1	chr12:47602203-47604544	NONHSAT027908

Variant related genes	Relation type
ENSG00000247774	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10881077	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10881079	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11183795	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183796	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12370622	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1554693	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17821774	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17822189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2004683	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2004684	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2111903	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2408718	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768144	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768782	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55711758	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55849521	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73110240	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs732523	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7974410	0.92[AMR][1000 genomes];0.96[EUR][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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47583200-47628600	Weak transcription	Aorta	Aorta
2	chr12:47584800-47605800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:47598800-47605000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:47599600-47605000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
5	chr12:47600000-47606200	Weak transcription	Adipose Nuclei	Adipose
6	chr12:47600000-47614600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:47600800-47614400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:47600800-47616400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:47601000-47606800	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr12:47601400-47606000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:47601400-47606200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:47601400-47610000	Weak transcription	HSMM	muscle
13	chr12:47601400-47610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:47601400-47612000	Weak transcription	Gastric	stomach
15	chr12:47601400-47616200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:47601600-47605800	Weak transcription	NHEK	skin
17	chr12:47601600-47610400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:47601600-47617400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:47601800-47628400	Weak transcription	Esophagus	oesophagus
20	chr12:47602000-47605800	Enhancers	A549	lung
21	chr12:47602000-47608600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:47602000-47615200	Weak transcription	Fetal Intestine Small	intestine
23	chr12:47602200-47606200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:47602200-47616600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:47602400-47605200	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
26	chr12:47602600-47616400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:47603000-47605400	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr12:47603000-47606000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr12:47603000-47608000	Weak transcription	Dnd41	blood
30	chr12:47603000-47608600	Weak transcription	Thymus	Thymus
31	chr12:47603000-47608800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:47603000-47609600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:47603200-47605800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr12:47603200-47606200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:47603200-47606400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:47603200-47608200	Weak transcription	Fetal Thymus	thymus
37	chr12:47603200-47611800	Weak transcription	Spleen	Spleen
38	chr12:47603200-47615600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:47603200-47616400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:47603600-47604800	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:47603800-47605800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:47603800-47608200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:47603800-47608200	Weak transcription	K562	blood
44	chr12:47604000-47605600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr12:47604000-47606000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:47604000-47608200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:47604200-47604600	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:47604200-47604800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:47604200-47605400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:47604200-47605400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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