Variant report

Variant	rs6580769
Chromosome Location	chr12:51195521-51195522
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	chr12:51194188..51196779-chr12:51231539..51234008,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10735827	0.88[EUR][1000 genomes]
rs10747586	1.00[ASN][1000 genomes]
rs10747592	0.88[EUR][1000 genomes]
rs10783377	1.00[ASN][1000 genomes]
rs10783380	1.00[ASN][1000 genomes]
rs10783388	0.88[EUR][1000 genomes]
rs1109726	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609941	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561422	0.89[EUR][1000 genomes]
rs2250751	1.00[ASN][1000 genomes]
rs2250752	1.00[ASN][1000 genomes]
rs2251024	1.00[ASN][1000 genomes]
rs2251603	1.00[ASN][1000 genomes]
rs2252589	1.00[ASN][1000 genomes]
rs2554862	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684889	1.00[ASN][1000 genomes]
rs2684898	1.00[ASN][1000 genomes]
rs2684900	1.00[ASN][1000 genomes]
rs2684901	1.00[ASN][1000 genomes]
rs2700479	1.00[ASN][1000 genomes]
rs2700480	1.00[ASN][1000 genomes]
rs2700482	1.00[ASN][1000 genomes]
rs2700485	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2731434	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2731439	1.00[ASN][1000 genomes]
rs2731440	1.00[ASN][1000 genomes]
rs2731442	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2731443	1.00[ASN][1000 genomes]
rs319942	1.00[JPT][hapmap]
rs4768862	0.86[EUR][1000 genomes]
rs57602501	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57729468	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66838741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66947035	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67218241	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67356137	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67934435	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135837	1.00[ASN][1000 genomes]
rs7305655	1.00[ASN][1000 genomes]
rs7307788	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487150	0.85[EUR][1000 genomes]
rs7958114	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7960015	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964642	0.87[EUR][1000 genomes]
rs7968440	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7976942	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977064	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977690	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7977742	0.84[AMR][1000 genomes]
rs7978559	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979165	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829112	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829114	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829115	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs865489	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580769	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51180800-51204400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:51188600-51207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:51189000-51195600	Strong transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:51189600-51195800	ZNF genes & repeats	GM12878-XiMat	blood
5	chr12:51189600-51196400	Strong transcription	HSMM	muscle
6	chr12:51189600-51199800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:51189800-51195600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:51190200-51204000	Weak transcription	Gastric	stomach
9	chr12:51190200-51215200	Weak transcription	Pancreas	Pancrea
10	chr12:51190600-51196400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:51190600-51197400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:51191400-51196600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
13	chr12:51191800-51195600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr12:51192400-51195800	ZNF genes & repeats	A549	lung
15	chr12:51192400-51195800	ZNF genes & repeats	Dnd41	blood
16	chr12:51193200-51196400	Strong transcription	Placenta	Placenta
17	chr12:51193200-51200000	Weak transcription	Thymus	Thymus
18	chr12:51193200-51200000	Weak transcription	Spleen	Spleen
19	chr12:51193200-51203200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:51193200-51204400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:51193200-51207600	Weak transcription	Fetal Heart	heart
22	chr12:51193200-51207800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:51193200-51207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:51193200-51207800	Weak transcription	Esophagus	oesophagus
25	chr12:51193200-51208000	Weak transcription	Small Intestine	intestine
26	chr12:51193200-51211200	Weak transcription	Aorta	Aorta
27	chr12:51193400-51195600	Strong transcription	Liver	Liver
28	chr12:51193400-51203200	Weak transcription	Colonic Mucosa	Colon
29	chr12:51193400-51204000	Weak transcription	Psoas Muscle	Psoas
30	chr12:51193400-51207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:51193600-51195800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr12:51193600-51195800	Strong transcription	Hela-S3	cervix
33	chr12:51193800-51202800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:51193800-51204200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:51193800-51204400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:51193800-51204400	Weak transcription	Fetal Brain Male	brain
37	chr12:51194000-51195800	Strong transcription	HepG2	liver
38	chr12:51194000-51200000	Weak transcription	Brain Anterior Caudate	brain
39	chr12:51194000-51200000	Weak transcription	K562	blood
40	chr12:51194000-51203200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:51194000-51203400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:51194000-51203400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:51194000-51204200	Weak transcription	NHLF	lung
44	chr12:51194000-51204400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:51194000-51204400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:51194000-51204400	Weak transcription	NHEK	skin
47	chr12:51194000-51204600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:51194200-51195600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:51194200-51195600	Strong transcription	Fetal Lung	lung
50	chr12:51194200-51196200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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