Variant report

Variant	rs4356312
Chromosome Location	chr12:105450773-105450774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10746010	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778367	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778368	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778369	0.85[EUR][1000 genomes]
rs1196742	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196745	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196749	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	1.00[ASN][1000 genomes]
rs1196754	1.00[ASN][1000 genomes]
rs1196756	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[ASN][1000 genomes]
rs1196764	0.82[EUR][1000 genomes]
rs1196765	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196798	0.82[EUR][1000 genomes]
rs1196800	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196805	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196806	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196807	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196808	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196811	0.82[EUR][1000 genomes]
rs1196813	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196819	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196820	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196823	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196825	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196831	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196833	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196839	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196841	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196848	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196851	0.82[EUR][1000 genomes]
rs1196853	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196861	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	0.82[EUR][1000 genomes]
rs1196871	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.82[EUR][1000 genomes]
rs1196873	0.82[EUR][1000 genomes]
rs1196874	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196881	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196885	0.83[AMR][1000 genomes]
rs1206559	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209308	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211276	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211277	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345096	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1621553	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[ASN][1000 genomes]
rs1663565	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166142	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2257156	0.82[EUR][1000 genomes]
rs2374449	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2440692	0.81[EUR][1000 genomes]
rs2440714	0.84[EUR][1000 genomes]
rs2440715	1.00[ASN][1000 genomes]
rs2440718	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464173	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464175	0.82[EUR][1000 genomes]
rs2464181	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	0.81[EUR][1000 genomes]
rs4356313	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372534	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964122	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964331	0.87[EUR][1000 genomes]
rs6539183	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6539186	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6539187	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539188	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7132040	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.85[EUR][1000 genomes]
rs7132855	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7299701	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7302854	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7303961	0.87[EUR][1000 genomes]
rs7963877	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs935240	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935242	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935246	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	0.82[EUR][1000 genomes]
rs935249	0.82[EUR][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4356312	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105409400-105465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr12:105413000-105476800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:105413200-105457800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:105414800-105454000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:105420000-105477000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:105423200-105459400	Weak transcription	Lung	lung
7	chr12:105431400-105461600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:105431800-105454800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:105432200-105454600	Weak transcription	NHEK	skin
10	chr12:105434000-105453000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:105435200-105453600	Weak transcription	Fetal Stomach	stomach
12	chr12:105435600-105467400	Weak transcription	Brain Substantia Nigra	brain
13	chr12:105441200-105477000	Weak transcription	Gastric	stomach
14	chr12:105441400-105453400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:105441400-105454800	Weak transcription	Pancreas	Pancrea
16	chr12:105441600-105458200	Weak transcription	Right Ventricle	heart
17	chr12:105442400-105451000	Weak transcription	Fetal Brain Male	brain
18	chr12:105442400-105469800	Weak transcription	Fetal Lung	lung
19	chr12:105443400-105465000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:105443800-105453000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:105444000-105453600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:105445200-105453200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:105445400-105453200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:105445800-105472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:105446800-105451200	Weak transcription	NHLF	lung
26	chr12:105447000-105453200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:105447000-105461600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:105447000-105464600	Weak transcription	Left Ventricle	heart
29	chr12:105447000-105468000	Weak transcription	K562	blood
30	chr12:105447000-105468600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:105447200-105462000	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:105447200-105466800	Weak transcription	Brain Angular Gyrus	brain
33	chr12:105447200-105477200	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:105447400-105451000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:105447400-105451200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:105447400-105454600	Weak transcription	Adipose Nuclei	Adipose
37	chr12:105447400-105458200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:105448200-105451400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:105448200-105461400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:105448400-105450800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:105448600-105452000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr12:105448800-105451400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:105448800-105454800	Strong transcription	HMEC	breast
44	chr12:105448800-105459800	Weak transcription	Ovary	ovary
45	chr12:105448800-105461200	Strong transcription	Osteobl	bone
46	chr12:105449000-105451600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:105449000-105455600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:105449000-105456800	Strong transcription	HSMM	muscle
49	chr12:105449200-105454800	Weak transcription	Aorta	Aorta
50	chr12:105449400-105450800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links