Variant report

Variant	rs12424943
Chromosome Location	chr12:104485278-104485279
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	chr12:104473419..104476228-chr12:104483759..104485884,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111727	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10507174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10507175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11111898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422505	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423684	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12426862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12427339	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12579268	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12582966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17035324	0.85[CHB][hapmap]
rs17192854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17805748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17805766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35142441	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812800	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3850022	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4129598	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs4131750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4131752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4246264	0.85[CHB][hapmap]
rs4340124	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4545635	0.85[CHB][hapmap]
rs4614534	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs4964219	0.87[ASN][1000 genomes]
rs4964260	0.85[CHB][hapmap]
rs4964627	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs59079741	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59644448	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61647968	0.85[ASN][1000 genomes]
rs61937639	1.00[ASN][1000 genomes]
rs61937641	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61937642	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61939180	0.85[ASN][1000 genomes]
rs61939183	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61939188	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61939190	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61939192	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61939195	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61939196	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61939198	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61939199	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61939200	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61939201	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7132418	0.86[CEU][hapmap]
rs7294997	0.82[CEU][hapmap]
rs7299866	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs73177987	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73177991	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7957725	0.86[CEU][hapmap]
rs7975161	0.85[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12424943	NFYB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104459800-104491800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:104460000-104496800	Weak transcription	HepG2	liver
3	chr12:104460000-104511800	Weak transcription	Hela-S3	cervix
4	chr12:104460000-104526200	Weak transcription	Colonic Mucosa	Colon
5	chr12:104461200-104492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:104470600-104486200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:104471000-104499600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr12:104471400-104500000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:104472000-104497400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:104472400-104486200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr12:104472400-104497400	Strong transcription	Placenta	Placenta
12	chr12:104472400-104501200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:104472600-104485400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:104472600-104485800	Strong transcription	Dnd41	blood
15	chr12:104472600-104497200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:104474400-104485800	Strong transcription	Osteobl	bone
17	chr12:104475800-104489400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:104476200-104485400	Strong transcription	HSMM	muscle
19	chr12:104476200-104497400	Strong transcription	Adipose Nuclei	Adipose
20	chr12:104476600-104486200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:104476600-104488200	Strong transcription	Fetal Lung	lung
22	chr12:104477000-104486200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:104477200-104508400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:104478200-104492800	Weak transcription	NHEK	skin
25	chr12:104478400-104492800	Weak transcription	Spleen	Spleen
26	chr12:104478600-104487600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:104478600-104487800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:104478600-104499400	Weak transcription	Fetal Heart	heart
29	chr12:104479600-104485800	Strong transcription	Fetal Thymus	thymus
30	chr12:104479600-104486200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:104479600-104486200	Strong transcription	Fetal Muscle Leg	muscle
32	chr12:104479600-104489000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:104479800-104485400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr12:104479800-104485600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:104479800-104485800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:104480000-104508400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:104480200-104485600	Strong transcription	NHDF-Ad	bronchial
38	chr12:104480200-104485800	Strong transcription	Liver	Liver
39	chr12:104480600-104485800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr12:104480600-104489600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:104480600-104497600	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:104481000-104495000	Weak transcription	Esophagus	oesophagus
43	chr12:104481000-104499400	Weak transcription	Stomach Mucosa	stomach
44	chr12:104481000-104500800	Weak transcription	K562	blood
45	chr12:104481200-104486000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:104481200-104492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:104481600-104485800	Strong transcription	Primary T cells from cord blood	blood
48	chr12:104481800-104486000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:104482200-104490800	Weak transcription	Brain Angular Gyrus	brain
50	chr12:104482400-104490000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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