Variant report

Variant	rs66479670
Chromosome Location	chr12:31650267-31650268
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:31650144-31650331	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31645681..31648505-chr12:31649831..31652317,2	MCF-7	breast:

Variant related genes	Relation type
DENND5B	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1038066	0.86[EUR][1000 genomes]
rs12809140	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12812075	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812141	1.00[ASN][1000 genomes]
rs12816170	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816386	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818749	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12819062	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12820294	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12821808	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822601	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825207	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12826193	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12831480	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17497517	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17497656	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17497998	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1879399	1.00[ASN][1000 genomes]
rs2126897	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34007930	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34094545	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34184789	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34271764	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34308937	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34450466	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585237	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34642866	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34667511	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34949976	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34955459	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34986122	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35029695	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193529	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35545963	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35567364	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35679974	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35692484	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850967	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4338625	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4930981	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4930983	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4931485	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931498	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931503	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931504	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931510	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4931518	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55635343	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55643034	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55771933	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56183451	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234529	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282720	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56327034	1.00[ASN][1000 genomes]
rs56409505	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66520413	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66552209	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66597773	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66635949	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67415228	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67963293	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68030436	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455664	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71455667	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71455668	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455669	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455670	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71455671	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73080503	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73084486	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73086471	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73088505	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088597	0.86[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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:31628800-31655800	Weak transcription	Gastric	stomach
3	chr12:31630400-31655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:31633000-31651600	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:31633000-31652400	Weak transcription	Fetal Brain Female	brain
6	chr12:31633200-31652200	Weak transcription	Adipose Nuclei	Adipose
7	chr12:31636200-31663000	Weak transcription	Aorta	Aorta
8	chr12:31639000-31655800	Weak transcription	Left Ventricle	heart
9	chr12:31640600-31650400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:31642600-31670000	Weak transcription	Fetal Lung	lung
11	chr12:31643600-31658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:31644400-31659400	Weak transcription	Pancreas	Pancrea
13	chr12:31645600-31658000	Weak transcription	Fetal Intestine Small	intestine
14	chr12:31645800-31651000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:31645800-31651000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:31646000-31650600	Weak transcription	Right Ventricle	heart
17	chr12:31646000-31651000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:31646000-31652000	Weak transcription	Brain Germinal Matrix	brain
19	chr12:31646000-31652400	Weak transcription	Fetal Kidney	kidney
20	chr12:31646000-31652600	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:31646000-31659400	Weak transcription	NH-A	brain
22	chr12:31646000-31659800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:31646200-31650600	Weak transcription	HSMM	muscle
24	chr12:31646200-31651000	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:31646200-31651200	Weak transcription	HUVEC	blood vessel
26	chr12:31646200-31651400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:31646200-31652600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:31646200-31657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:31647000-31652200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:31647400-31650400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:31647400-31660000	Weak transcription	Psoas Muscle	Psoas
32	chr12:31647600-31650400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:31647600-31650400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:31647600-31650400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:31647600-31652600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:31647600-31661200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:31647800-31651200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:31647800-31653400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:31647800-31661400	Weak transcription	Brain Angular Gyrus	brain
40	chr12:31648000-31650400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:31648000-31650800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr12:31648200-31651000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr12:31648200-31651200	Weak transcription	Liver	Liver
44	chr12:31648200-31651200	Weak transcription	HepG2	liver
45	chr12:31648600-31651600	Enhancers	Hela-S3	cervix
46	chr12:31648800-31650400	Weak transcription	GM12878-XiMat	blood
47	chr12:31648800-31651000	Weak transcription	Fetal Intestine Large	intestine
48	chr12:31648800-31652200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:31648800-31657200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:31649000-31650400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links