Variant report

Variant	rs57729468
Chromosome Location	chr12:51176673-51176674
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51155325..51162343-chr12:51172009..51182370,14	MCF-7	breast:
2	chr12:51171915..51173515-chr12:51175788..51178254,2	MCF-7	breast:
3	chr12:51175977..51178519-chr12:51179089..51181352,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10735827	0.87[EUR][1000 genomes]
rs10747586	1.00[ASN][1000 genomes]
rs10747592	0.87[EUR][1000 genomes]
rs10783377	1.00[ASN][1000 genomes]
rs10783380	1.00[ASN][1000 genomes]
rs10783388	0.87[EUR][1000 genomes]
rs1109726	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609231	1.00[ASN][1000 genomes]
rs11609941	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832315	1.00[ASN][1000 genomes]
rs1561422	0.85[EUR][1000 genomes]
rs2250751	1.00[ASN][1000 genomes]
rs2250752	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2251024	1.00[ASN][1000 genomes]
rs2251603	1.00[ASN][1000 genomes]
rs2252589	1.00[ASN][1000 genomes]
rs2554862	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[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	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2731434	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2731439	1.00[ASN][1000 genomes]
rs2731440	1.00[ASN][1000 genomes]
rs2731442	1.00[ASN][1000 genomes]
rs2731443	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4768862	0.83[EUR][1000 genomes]
rs56089074	1.00[ASN][1000 genomes]
rs57602501	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580769	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66597435	1.00[ASN][1000 genomes]
rs66644594	1.00[ASN][1000 genomes]
rs66838741	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66947035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67218241	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67356137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67934435	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68171620	1.00[ASN][1000 genomes]
rs7135837	1.00[ASN][1000 genomes]
rs7305655	1.00[ASN][1000 genomes]
rs7307788	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487150	0.86[EUR][1000 genomes]
rs7958114	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7960015	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964642	0.84[EUR][1000 genomes]
rs7968440	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7976942	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977064	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977690	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7977742	0.85[AMR][1000 genomes]
rs7978559	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979165	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829112	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829114	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829115	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs865489	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3497481	chr12:51150734-51185125	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
2	esv3497482	chr12:51151798-51185232	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
3	esv3386327	chr12:51154734-51184232	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
4	nsv899077	chr12:51160612-51188397	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	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
rs57729468	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51159000-51180200	Weak transcription	Esophagus	oesophagus
2	chr12:51159200-51179400	Weak transcription	Aorta	Aorta
3	chr12:51159200-51192600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:51159400-51192600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:51159600-51189200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:51159800-51178200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:51159800-51178400	Weak transcription	NHDF-Ad	bronchial
8	chr12:51159800-51180600	Weak transcription	Fetal Lung	lung
9	chr12:51159800-51189600	Weak transcription	Spleen	Spleen
10	chr12:51159800-51190400	Weak transcription	Fetal Kidney	kidney
11	chr12:51159800-51191200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:51160000-51179200	Weak transcription	HSMMtube	muscle
13	chr12:51160000-51179800	Weak transcription	Small Intestine	intestine
14	chr12:51160000-51189800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:51160000-51190800	Weak transcription	Right Ventricle	heart
16	chr12:51160200-51178200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:51160200-51178400	Weak transcription	HMEC	breast
18	chr12:51160200-51179400	Weak transcription	Right Atrium	heart
19	chr12:51160200-51180200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:51160200-51189600	Weak transcription	Pancreas	Pancrea
21	chr12:51160200-51189800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:51160600-51178200	Weak transcription	Psoas Muscle	Psoas
23	chr12:51160800-51189600	Weak transcription	Brain Angular Gyrus	brain
24	chr12:51160800-51190600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:51161000-51178200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:51161000-51189800	Weak transcription	Ovary	ovary
27	chr12:51161800-51180400	Weak transcription	Colonic Mucosa	Colon
28	chr12:51162400-51179200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:51162600-51178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:51163000-51178000	Weak transcription	A549	lung
31	chr12:51163000-51178400	Weak transcription	NHEK	skin
32	chr12:51163200-51179800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:51164400-51189600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:51165200-51179200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:51165400-51177000	Weak transcription	Dnd41	blood
36	chr12:51165400-51179800	Weak transcription	Brain Germinal Matrix	brain
37	chr12:51166000-51179200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:51166800-51178200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:51166800-51178200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:51166800-51178400	Weak transcription	Thymus	Thymus
41	chr12:51166800-51179600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr12:51167000-51178200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:51167000-51180400	Weak transcription	Fetal Brain Female	brain
44	chr12:51167200-51179800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:51167800-51179200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:51168400-51179200	Weak transcription	GM12878-XiMat	blood
47	chr12:51169000-51178200	Genic enhancers	Hela-S3	cervix
48	chr12:51171600-51177800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:51172600-51190600	Weak transcription	Fetal Brain Male	brain
50	chr12:51172800-51179400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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