Variant report

Variant	rs6580730
Chromosome Location	chr12:50623173-50623174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50622031..50624190-chr12:50625065..50627744,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10783344	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10876013	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169314	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11169315	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11169317	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169319	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11169322	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169331	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169332	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169335	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169339	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11169359	0.80[ASN][1000 genomes]
rs12424691	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12424713	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12425229	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12425705	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12811291	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12823506	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12828340	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1362983	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17124562	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1972611	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2009072	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2302900	0.81[AMR][1000 genomes]
rs2358539	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34825838	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35768991	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3812825	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3861100	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7132551	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71465002	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7308095	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7308885	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7314465	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7486747	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7953953	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7979830	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6580730	CERS5	cis	Nerve Tibial	GTEx
rs6580730	DIP2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50599800-50635800	Weak transcription	Pancreas	Pancrea
2	chr12:50609200-50633200	Weak transcription	Small Intestine	intestine
3	chr12:50616200-50633200	Weak transcription	Lung	lung
4	chr12:50616400-50628400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:50616400-50632000	Weak transcription	Fetal Brain Male	brain
6	chr12:50616400-50634000	Weak transcription	Gastric	stomach
7	chr12:50616400-50634000	Weak transcription	Ovary	ovary
8	chr12:50616400-50636200	Weak transcription	Left Ventricle	heart
9	chr12:50616600-50628200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:50616600-50632200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:50616600-50634000	Weak transcription	Colonic Mucosa	Colon
12	chr12:50616600-50634000	Weak transcription	Psoas Muscle	Psoas
13	chr12:50616600-50634000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:50616800-50625200	Weak transcription	Brain Substantia Nigra	brain
15	chr12:50616800-50626800	Weak transcription	Fetal Kidney	kidney
16	chr12:50616800-50636400	Weak transcription	Aorta	Aorta
17	chr12:50616800-50641600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
19	chr12:50617000-50626800	Weak transcription	Adipose Nuclei	Adipose
20	chr12:50617000-50632800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:50617000-50634000	Weak transcription	NHLF	lung
22	chr12:50617000-50636200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:50617200-50628400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:50617200-50633000	Strong transcription	Fetal Intestine Small	intestine
25	chr12:50617400-50626800	Weak transcription	Fetal Lung	lung
26	chr12:50617400-50634600	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:50617400-50635600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:50617600-50638400	Weak transcription	Brain Germinal Matrix	brain
29	chr12:50618400-50624600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:50618400-50625200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:50618600-50623600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:50618600-50625000	Weak transcription	HSMMtube	muscle
33	chr12:50618600-50626800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:50618600-50627000	Weak transcription	Stomach Mucosa	stomach
35	chr12:50618600-50628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:50618600-50628400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:50618600-50628400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:50618600-50628400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:50618600-50633800	Weak transcription	NHDF-Ad	bronchial
40	chr12:50618600-50634000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:50618600-50634000	Weak transcription	Osteobl	bone
42	chr12:50618600-50634400	Weak transcription	HSMM	muscle
43	chr12:50618600-50636200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:50618600-50638400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:50618600-50640000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:50618800-50626200	Weak transcription	Hela-S3	cervix
47	chr12:50619000-50626600	Weak transcription	GM12878-XiMat	blood
48	chr12:50619000-50628000	Weak transcription	Placenta	Placenta
49	chr12:50619400-50625400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr12:50619400-50626200	Strong transcription	Fetal Intestine Large	intestine

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