Variant report

Variant	rs10736030
Chromosome Location	chr12:47428978-47428979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47426514..47428986-chr12:47432819..47435080,2	K562	blood:
2	chr12:47427484..47430448-chr12:47461043..47464291,4	MCF-7	breast:
3	chr12:47424715..47431022-chr12:47469878..47476557,9	MCF-7	breast:
4	chr12:47423549..47426668-chr12:47427215..47430937,3	K562	blood:

Variant related genes	Relation type
ENSG00000179715	Chromatin interaction
ENSG00000139211	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10748457	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10748458	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10748460	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10785650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10785653	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881024	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881027	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10881029	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10881030	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881031	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881033	0.94[EUR][1000 genomes]
rs1557781	0.96[EUR][1000 genomes]
rs17097518	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs1859112	0.98[EUR][1000 genomes]
rs2158133	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214335	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2408711	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2711698	0.95[EUR][1000 genomes]
rs2711713	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768769	0.99[ASN][1000 genomes]
rs4768771	1.00[YRI][hapmap]
rs7133990	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7136412	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139043	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311552	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757149	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757150	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7956056	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7956758	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7958499	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7961460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7976595	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8181633	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854889	1.00[YRI][hapmap]
rs886315	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs886317	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10736030	CCNT1	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47426600-47429000	Enhancers	HMEC	breast
2	chr12:47426600-47429000	Enhancers	HSMM	muscle
3	chr12:47426600-47429000	Enhancers	NH-A	brain
4	chr12:47426600-47429200	Enhancers	Colon Smooth Muscle	Colon
5	chr12:47426600-47429200	Flanking Active TSS	A549	lung
6	chr12:47426600-47429600	Enhancers	Hela-S3	cervix
7	chr12:47426600-47429800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr12:47426800-47429000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:47426800-47429000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr12:47426800-47429000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:47426800-47429400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr12:47426800-47429400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:47426800-47429400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:47426800-47429800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr12:47427000-47429000	Enhancers	Ovary	ovary
16	chr12:47427000-47429400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:47427000-47429600	Enhancers	Fetal Intestine Large	intestine
18	chr12:47427200-47429400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:47427400-47429000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:47427400-47429200	Enhancers	Fetal Intestine Small	intestine
21	chr12:47427600-47429000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:47427800-47429200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:47427800-47431800	Weak transcription	Liver	Liver
24	chr12:47428200-47429000	Enhancers	H9 Cell Line	embryonic stem cell
25	chr12:47428400-47429000	Enhancers	Pancreas	Pancrea
26	chr12:47428400-47429000	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr12:47428400-47431400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:47428600-47429000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:47428600-47429000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:47428600-47429000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:47428600-47429000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:47428600-47429000	Weak transcription	Fetal Kidney	kidney
33	chr12:47428600-47429400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:47428600-47431800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:47428800-47429000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr12:47428800-47429200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:47428800-47433000	Weak transcription	Osteobl	bone

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