Variant report

Variant	rs17123924
Chromosome Location	chr12:50146765-50146766
allele	A/G
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	POLR2A	chr12:50146396-50148700	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50144547..50147013-chr12:50560890..50562715,2	MCF-7	breast:

Variant related genes	Relation type
TMBIM6	TF binding region
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10128824	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169110	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169114	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169115	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169120	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297814	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299751	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300919	0.83[AFR][1000 genomes]
rs12300962	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12306951	1.00[AMR][1000 genomes]
rs12310580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12312112	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313681	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314036	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12315508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12317162	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320895	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1317263	1.00[AMR][1000 genomes]
rs17119738	1.00[AMR][1000 genomes]
rs17123787	1.00[AMR][1000 genomes]
rs17123827	1.00[AMR][1000 genomes]
rs17123879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9804867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9805090	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50137000-50147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:50137200-50152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:50137400-50150800	Weak transcription	Fetal Brain Male	brain
4	chr12:50141400-50146800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:50142200-50148200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:50144000-50146800	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr12:50144000-50146800	Weak transcription	Lung	lung
8	chr12:50144000-50151600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:50144200-50146800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:50144200-50148800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr12:50144400-50146800	Weak transcription	Esophagus	oesophagus
12	chr12:50144400-50146800	Weak transcription	Gastric	stomach
13	chr12:50144400-50147000	Weak transcription	Pancreas	Pancrea
14	chr12:50144400-50147600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:50144600-50146800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:50144600-50146800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:50144600-50146800	Weak transcription	Right Ventricle	heart
18	chr12:50144600-50146800	Weak transcription	Spleen	Spleen
19	chr12:50144600-50148000	Weak transcription	Right Atrium	heart
20	chr12:50144800-50146800	Weak transcription	Aorta	Aorta
21	chr12:50144800-50146800	Enhancers	Colon Smooth Muscle	Colon
22	chr12:50144800-50146800	Weak transcription	Left Ventricle	heart
23	chr12:50144800-50146800	Weak transcription	Psoas Muscle	Psoas
24	chr12:50144800-50147000	Weak transcription	Small Intestine	intestine
25	chr12:50144800-50147200	Enhancers	Fetal Heart	heart
26	chr12:50144800-50148000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:50145000-50146800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:50145000-50156000	Strong transcription	Dnd41	blood
29	chr12:50145000-50157000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:50145000-50159200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:50145200-50146800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:50145200-50147000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:50145200-50149600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr12:50145200-50149600	Strong transcription	Hela-S3	cervix
35	chr12:50145200-50149600	Strong transcription	K562	blood
36	chr12:50145200-50149600	Strong transcription	NHEK	skin
37	chr12:50145400-50146800	Genic enhancers	GM12878-XiMat	blood
38	chr12:50145600-50149800	Strong transcription	HepG2	liver
39	chr12:50145800-50159200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:50146000-50147000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:50146000-50148000	Genic enhancers	Monocytes-CD14+_RO01746	blood
42	chr12:50146000-50148800	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr12:50146000-50149600	Genic enhancers	Liver	Liver
44	chr12:50146000-50151000	Weak transcription	Stomach Mucosa	stomach
45	chr12:50146000-50157000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr12:50146000-50159000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:50146000-50159000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:50146000-50159000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:50146200-50146800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:50146200-50146800	Strong transcription	Muscle Satellite Cultured Cells	--

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