Variant report

Variant	rs11176069
Chromosome Location	chr12:66561804-66561805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66561525..66563608-chr12:66580703..66583177,2	K562	blood:
2	chr12:66523792..66527078-chr12:66561013..66565049,6	MCF-7	breast:
3	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
4	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:
5	chr12:66561184..66563224-chr12:66629023..66631827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239335	Chromatin interaction
ENSG00000139233	Chromatin interaction
ENSG00000266539	Chromatin interaction
ENSG00000090376	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11176074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176075	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176084	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11465939	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11465961	0.85[EUR][1000 genomes]
rs11465965	0.85[EUR][1000 genomes]
rs1168743	1.00[ASN][1000 genomes]
rs11836532	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297278	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311209	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17102065	1.00[ASN][1000 genomes]
rs17102070	1.00[ASN][1000 genomes]
rs17102107	1.00[EUR][1000 genomes]
rs17102243	0.85[EUR][1000 genomes]
rs17767394	0.85[EUR][1000 genomes]
rs1797411	1.00[ASN][1000 genomes]
rs1921081	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967338	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34557475	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61387333	1.00[EUR][1000 genomes]
rs7307195	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960539	1.00[ASN][1000 genomes]
rs7963270	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv541516	chr12:66547969-66596036	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv899215	chr12:66556960-66594134	Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:66536400-66562400	Weak transcription	HMEC	breast
3	chr12:66539400-66562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:66547400-66562000	Weak transcription	HUVEC	blood vessel
6	chr12:66548400-66562200	Weak transcription	Brain Anterior Caudate	brain
7	chr12:66548600-66562000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:66553000-66562200	Weak transcription	Brain Angular Gyrus	brain
9	chr12:66553200-66562400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:66554000-66562000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:66554000-66562000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:66554000-66562000	Weak transcription	NHEK	skin
13	chr12:66554000-66562000	Weak transcription	Osteobl	bone
14	chr12:66554000-66562200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:66554000-66562200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:66554000-66562200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:66554000-66562200	Weak transcription	NHLF	lung
18	chr12:66554000-66562400	Weak transcription	Brain Germinal Matrix	brain
19	chr12:66554000-66563000	Weak transcription	Gastric	stomach
20	chr12:66554200-66562200	Weak transcription	NH-A	brain
21	chr12:66554400-66562000	Weak transcription	Fetal Kidney	kidney
22	chr12:66554600-66562000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:66554800-66562200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:66555000-66562200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:66555000-66562600	Weak transcription	Aorta	Aorta
26	chr12:66555000-66562800	Weak transcription	Esophagus	oesophagus
27	chr12:66555200-66562200	Weak transcription	Fetal Stomach	stomach
28	chr12:66556400-66562400	Weak transcription	Spleen	Spleen
29	chr12:66556600-66562200	Weak transcription	Brain Substantia Nigra	brain
30	chr12:66557000-66562800	Weak transcription	Ovary	ovary
31	chr12:66558200-66562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:66558400-66562400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:66559400-66562400	Weak transcription	Colonic Mucosa	Colon
34	chr12:66559400-66563000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:66559600-66562000	Weak transcription	Fetal Intestine Large	intestine
36	chr12:66559600-66562200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:66559800-66562000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:66560200-66562200	Weak transcription	Fetal Intestine Small	intestine
39	chr12:66560400-66562600	Enhancers	HepG2	liver
40	chr12:66560600-66562200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:66560600-66562200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr12:66560800-66562000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:66560800-66562200	Enhancers	Liver	Liver
44	chr12:66560800-66562400	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr12:66560800-66562400	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr12:66560800-66562400	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:66561000-66562000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:66561000-66562000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:66561000-66562000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:66561000-66562200	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links