Variant report

Variant	rs10861409
Chromosome Location	chr12:105760786-105760787
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10507190	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10861371	1.00[CHB][hapmap]
rs10861400	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10861403	0.87[EUR][1000 genomes]
rs10861407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861412	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861413	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112434	1.00[CHB][hapmap]
rs11112469	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11112470	0.81[EUR][1000 genomes]
rs11112473	0.80[EUR][1000 genomes]
rs11112475	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs11112478	0.82[EUR][1000 genomes]
rs11112480	0.82[EUR][1000 genomes]
rs11112482	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs11112483	0.85[EUR][1000 genomes]
rs11112484	0.87[EUR][1000 genomes]
rs11112485	0.85[EUR][1000 genomes]
rs11112486	0.87[EUR][1000 genomes]
rs11112487	0.87[EUR][1000 genomes]
rs11112488	0.87[EUR][1000 genomes]
rs11112492	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112493	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112494	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112495	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112496	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112497	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112498	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112499	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112502	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112504	0.94[EUR][1000 genomes]
rs11112505	0.94[EUR][1000 genomes]
rs11112506	0.94[EUR][1000 genomes]
rs1196748	1.00[CHB][hapmap]
rs1196749	1.00[CHB][hapmap]
rs1196753	1.00[CHB][hapmap]
rs1196754	1.00[CHB][hapmap]
rs1196756	1.00[CHB][hapmap]
rs1196760	1.00[CHB][hapmap]
rs1196777	1.00[CHB][hapmap]
rs1196793	1.00[CHB][hapmap]
rs1196852	1.00[CHB][hapmap]
rs1196861	1.00[CHB][hapmap]
rs1196862	1.00[CHB][hapmap]
rs1196864	1.00[CHB][hapmap]
rs12371845	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12819965	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12820423	0.94[EUR][1000 genomes]
rs12822081	1.00[CHB][hapmap]
rs12829692	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12829741	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12831150	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1432592	0.81[EUR][1000 genomes]
rs17036960	0.82[EUR][1000 genomes]
rs17041538	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2440715	1.00[CHB][hapmap]
rs2888846	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs34346262	0.87[EUR][1000 genomes]
rs35335704	0.81[EUR][1000 genomes]
rs35519603	0.82[EUR][1000 genomes]
rs4545651	1.00[CHB][hapmap]
rs6797	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7131942	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7299225	1.00[CHB][hapmap]
rs7302174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181878	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7954485	0.81[EUR][1000 genomes]
rs7959385	1.00[CHB][hapmap]
rs7968892	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7969370	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7969665	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7972183	0.81[EUR][1000 genomes]
rs935240	1.00[CHB][hapmap]
rs935241	1.00[CHB][hapmap]
rs935244	1.00[CHB][hapmap]
rs9645790	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9645791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][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	nsv899500	chr12:105742674-105803028	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10861409	C12orf75	cis	Artery Aorta	GTEx
rs10861409	C12orf75	cis	Artery Tibial	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105734800-105776600	Weak transcription	Esophagus	oesophagus
2	chr12:105735000-105776600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:105735600-105766800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:105735600-105776600	Weak transcription	Fetal Intestine Small	intestine
5	chr12:105746000-105776800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:105747000-105762000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:105747000-105772600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:105747000-105773200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:105747200-105761400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:105747200-105766000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:105747400-105761800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:105747400-105762000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:105748000-105776600	Weak transcription	Gastric	stomach
14	chr12:105748800-105776800	Weak transcription	Pancreas	Pancrea
15	chr12:105749600-105762600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:105749600-105763800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:105749800-105765600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:105750000-105762600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:105751000-105769000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:105751200-105766200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:105751200-105776800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:105751400-105762600	Weak transcription	HSMMtube	muscle
23	chr12:105751400-105775200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:105752000-105762400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:105752200-105765000	Weak transcription	Stomach Mucosa	stomach
26	chr12:105752400-105776400	Weak transcription	Aorta	Aorta
27	chr12:105752600-105769000	Strong transcription	Dnd41	blood
28	chr12:105754000-105764200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:105754200-105762000	Weak transcription	GM12878-XiMat	blood
30	chr12:105754200-105763800	Weak transcription	NHEK	skin
31	chr12:105754200-105766400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:105754400-105761600	Weak transcription	NHLF	lung
33	chr12:105754600-105766600	Weak transcription	Fetal Stomach	stomach
34	chr12:105754800-105764000	Weak transcription	Thymus	Thymus
35	chr12:105755600-105762000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:105755600-105764400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:105755800-105762000	Weak transcription	Fetal Thymus	thymus
38	chr12:105755800-105762600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:105757200-105763800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:105758400-105761000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:105758400-105762400	Weak transcription	Osteobl	bone
42	chr12:105758400-105764400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr12:105758800-105769800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:105759200-105761400	Strong transcription	A549	lung
45	chr12:105759200-105761800	Strong transcription	NHDF-Ad	bronchial
46	chr12:105759200-105767800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:105759400-105761000	Strong transcription	NH-A	brain
48	chr12:105759600-105760800	Strong transcription	HUVEC	blood vessel
49	chr12:105759800-105762600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:105759800-105763400	Weak transcription	Primary T cells fromperipheralblood	blood

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