Variant report

Variant	rs17822189
Chromosome Location	chr12:47602995-47602996
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47598802..47603269-chr12:47603355..47607825,7	K562	blood:
2	chr12:47602204..47603894-chr12:47609005..47611921,2	K562	blood:
3	chr12:47602136..47604410-chr12:47609370..47611467,2	MCF-7	breast:

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
ENSG00000179715	Chromatin interaction
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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881079	0.93[CHB][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183795	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183796	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11183799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12370622	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1554693	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17821774	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2004683	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2004684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111903	0.88[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2408718	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768144	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768782	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[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];0.90[EUR][1000 genomes]
rs73110240	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974410	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[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:70 , 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	chr12:47599000-47603400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:47599600-47605000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
6	chr12:47599800-47603200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:47600000-47606200	Weak transcription	Adipose Nuclei	Adipose
8	chr12:47600000-47614600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:47600600-47603000	Enhancers	Duodenum Mucosa	Duodenum
10	chr12:47600600-47603000	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr12:47600600-47603800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
12	chr12:47600800-47603200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:47600800-47614400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:47600800-47616400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:47601000-47603200	Enhancers	K562	blood
16	chr12:47601000-47606800	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr12:47601400-47603000	Weak transcription	Left Ventricle	heart
18	chr12:47601400-47603400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:47601400-47603600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:47601400-47606000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:47601400-47606200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:47601400-47610000	Weak transcription	HSMM	muscle
23	chr12:47601400-47610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:47601400-47612000	Weak transcription	Gastric	stomach
25	chr12:47601400-47616200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:47601600-47605800	Weak transcription	NHEK	skin
27	chr12:47601600-47610400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:47601600-47617400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:47601800-47604200	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
30	chr12:47601800-47628400	Weak transcription	Esophagus	oesophagus
31	chr12:47602000-47603000	Enhancers	Fetal Muscle Trunk	muscle
32	chr12:47602000-47603600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr12:47602000-47604000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:47602000-47605800	Enhancers	A549	lung
35	chr12:47602000-47608600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr12:47602000-47615200	Weak transcription	Fetal Intestine Small	intestine
37	chr12:47602200-47603000	Enhancers	Small Intestine	intestine
38	chr12:47602200-47603000	Enhancers	Dnd41	blood
39	chr12:47602200-47603000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr12:47602200-47603600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:47602200-47603600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr12:47602200-47603800	Enhancers	Primary hematopoietic stem cells	blood
43	chr12:47602200-47604000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr12:47602200-47604200	Genic enhancers	Primary B cells from cord blood	blood
45	chr12:47602200-47604200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:47602200-47604200	Enhancers	GM12878-XiMat	blood
47	chr12:47602200-47606200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:47602200-47616600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:47602400-47605200	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
50	chr12:47602600-47603000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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