Variant report

Variant	rs12810794
Chromosome Location	chr12:29935240-29935241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10743672	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10743673	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10743674	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771578	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10771579	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10771580	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843501	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10843502	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10843503	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843504	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11609828	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12231167	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1551930	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2882467	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs302335	0.85[AMR][1000 genomes]
rs302336	0.85[AMR][1000 genomes]
rs302337	0.85[AMR][1000 genomes]
rs302338	0.86[AMR][1000 genomes]
rs4244848	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4244849	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931215	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931216	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4931217	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931218	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4931219	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931220	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56703053	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67168837	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7967779	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv898953	chr12:29905322-29989292	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv826294	chr12:29934604-29940372	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12810794	TMTC1	cis	Whole Blood	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29933000-29937800	Active TSS	Aorta	Aorta
2	chr12:29933800-29937800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:29934000-29935600	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr12:29934000-29936400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr12:29934000-29937800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr12:29934000-29937800	Active TSS	Fetal Kidney	kidney
7	chr12:29934000-29937800	Active TSS	NHLF	lung
8	chr12:29934000-29938000	Active TSS	Right Ventricle	heart
9	chr12:29934200-29935400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:29934200-29935600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
11	chr12:29934200-29935800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:29934200-29937400	Active TSS	Lung	lung
13	chr12:29934200-29937600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
14	chr12:29934200-29937600	Active TSS	Rectal Smooth Muscle	rectum
15	chr12:29934200-29937800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:29934400-29935400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
17	chr12:29934400-29935600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr12:29934400-29936400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:29934400-29937600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:29934400-29937600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:29934400-29937600	Bivalent/Poised TSS	Thymus	Thymus
22	chr12:29934400-29937800	Active TSS	Brain Anterior Caudate	brain
23	chr12:29934400-29937800	Active TSS	Brain Hippocampus Middle	brain
24	chr12:29934400-29937800	Active TSS	Fetal Brain Female	brain
25	chr12:29934600-29936600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:29934600-29937400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr12:29934600-29937800	Active TSS	Right Atrium	heart
28	chr12:29934600-29937800	Active TSS	Stomach Smooth Muscle	stomach
29	chr12:29934800-29935400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:29934800-29935400	Active TSS	Brain Germinal Matrix	brain
31	chr12:29934800-29935400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr12:29934800-29935400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr12:29934800-29935400	Flanking Active TSS	Osteobl	bone
34	chr12:29934800-29935600	Active TSS	Fetal Muscle Trunk	muscle
35	chr12:29934800-29936600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:29934800-29937400	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr12:29934800-29937400	Bivalent/Poised TSS	NHEK	skin
38	chr12:29934800-29937600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:29934800-29937600	Active TSS	Brain Cingulate Gyrus	brain
40	chr12:29934800-29937600	Active TSS	Brain Substantia Nigra	brain
41	chr12:29934800-29937800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:29934800-29937800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr12:29934800-29937800	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr12:29934800-29937800	Active TSS	Left Ventricle	heart
45	chr12:29934800-29937800	Active TSS	Ovary	ovary
46	chr12:29934800-29937800	Active TSS	Psoas Muscle	Psoas
47	chr12:29934800-29937800	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr12:29934800-29937800	Active TSS	HSMM	muscle
49	chr12:29935000-29935600	Active TSS	Fetal Brain Male	brain
50	chr12:29935000-29936400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links