Variant report

Variant	rs10783416
Chromosome Location	chr12:51577878-51577879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51577036..51579030-chr12:51592102..51594138,2	MCF-7	breast:
2	chr12:51476851..51477436-chr12:51577236..51578176,2	MCF-7	breast:
3	chr12:51577327..51580829-chr12:51630464..51634140,3	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10783414	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10783417	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876143	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10876146	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1565721	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1985457	0.81[EUR][1000 genomes]
rs2029686	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2436645	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2436646	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2436647	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2640511	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2640521	0.80[EUR][1000 genomes]
rs2640523	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2730647	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2730650	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2730654	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2956428	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6580799	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6580800	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6580801	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6580803	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580804	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306522	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959378	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10783416	DDN	cis	cerebellum	SCAN
rs10783416	TFCP2	cis	cerebellum	SCAN
rs10783416	CSRNP2	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51567400-51583400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:51567400-51584000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:51567400-51610600	Weak transcription	Right Atrium	heart
4	chr12:51574800-51583400	Weak transcription	Aorta	Aorta
5	chr12:51575600-51583600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:51575800-51583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:51576800-51578800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr12:51576800-51580800	Enhancers	Fetal Muscle Leg	muscle
9	chr12:51577000-51578200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr12:51577000-51578400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:51577200-51578000	Enhancers	Brain Cingulate Gyrus	brain
12	chr12:51577200-51578000	Enhancers	GM12878-XiMat	blood
13	chr12:51577200-51578200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:51577200-51578200	Enhancers	Fetal Kidney	kidney
15	chr12:51577400-51578000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:51577400-51578000	Enhancers	Brain Hippocampus Middle	brain
17	chr12:51577400-51578200	Enhancers	Fetal Heart	heart
18	chr12:51577400-51578200	Enhancers	K562	blood
19	chr12:51577400-51578400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:51577400-51578400	Enhancers	HSMM	muscle
21	chr12:51577600-51578000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:51577600-51578000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:51577600-51578200	Enhancers	Brain Germinal Matrix	brain
24	chr12:51577600-51578200	Enhancers	Fetal Lung	lung
25	chr12:51577600-51578200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:51577600-51578400	Enhancers	Psoas Muscle	Psoas
27	chr12:51577600-51582400	Weak transcription	Brain Substantia Nigra	brain
28	chr12:51577600-51583000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:51577800-51578000	Enhancers	Left Ventricle	heart
30	chr12:51577800-51578000	Enhancers	Ovary	ovary
31	chr12:51577800-51578000	Enhancers	Pancreas	Pancrea
32	chr12:51577800-51578000	Enhancers	HSMMtube	muscle
33	chr12:51577800-51578200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr12:51577800-51579600	Weak transcription	Fetal Thymus	thymus
35	chr12:51577800-51580200	Enhancers	HepG2	liver
36	chr12:51577800-51580600	Weak transcription	Fetal Stomach	stomach
37	chr12:51577800-51582000	Weak transcription	Brain Anterior Caudate	brain
38	chr12:51577800-51583400	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links