Variant report

Variant	rs10459204
Chromosome Location	chr12:105461620-105461621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:105461127-105461783	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105461590..105464324-chr12:105467653..105469817,3	K562	blood:
2	chr12:105458598..105460587-chr12:105460604..105462776,2	K562	blood:

Variant related genes	Relation type
ENSG00000257886	TF binding region
ALDH1L2	TF binding region
ENSG00000136010	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1014502	0.82[CEU][hapmap]
rs10459164	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10459203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861338	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861359	0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap]
rs10861361	0.82[CEU][hapmap];0.93[MEX][hapmap]
rs11112355	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112360	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11112363	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112364	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112370	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs11112376	0.82[CEU][hapmap]
rs11112412	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs11112416	0.82[CEU][hapmap]
rs11112421	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs11112432	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs11831854	0.82[CEU][hapmap]
rs12228093	0.82[CEU][hapmap]
rs12230762	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12815031	0.80[CEU][hapmap]
rs12823614	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12830078	0.80[ASN][1000 genomes]
rs1317955	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs1373552	0.82[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs1444611	0.82[CEU][hapmap]
rs17036625	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2166143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2272495	0.82[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap]
rs2293643	0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap]
rs2293644	0.82[CEU][hapmap]
rs34119882	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34384505	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34891908	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35073181	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35132501	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3794223	0.81[CEU][hapmap]
rs3794227	0.87[CEU][hapmap];1.00[MEX][hapmap]
rs3817607	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs4964121	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4964336	0.81[CEU][hapmap]
rs55908437	0.80[ASN][1000 genomes]
rs755604	0.82[CEU][hapmap]
rs881279	0.82[CEU][hapmap];1.00[MEX][hapmap]

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	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
4	esv1010041	chr12:105459777-105467603	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10459204	C12orf75	cis	cerebellum	SCAN
rs10459204	TCP11L2	cis	parietal	SCAN
rs10459204	KIAA1033	cis	cerebellum	SCAN

Chromatin state (count:59 , 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	chr12:105420000-105477000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr12:105435600-105467400	Weak transcription	Brain Substantia Nigra	brain
5	chr12:105441200-105477000	Weak transcription	Gastric	stomach
6	chr12:105442400-105469800	Weak transcription	Fetal Lung	lung
7	chr12:105443400-105465000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:105445800-105472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:105447000-105464600	Weak transcription	Left Ventricle	heart
10	chr12:105447000-105468000	Weak transcription	K562	blood
11	chr12:105447000-105468600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:105447200-105462000	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:105447200-105466800	Weak transcription	Brain Angular Gyrus	brain
14	chr12:105447200-105477200	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:105449400-105476800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:105450600-105461800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:105450800-105468200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:105452000-105464200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:105452000-105466200	Weak transcription	GM12878-XiMat	blood
20	chr12:105452200-105462000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:105453400-105476800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:105454200-105476600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:105455600-105465200	Strong transcription	HMEC	breast
24	chr12:105455600-105467800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:105455600-105476400	Weak transcription	Fetal Brain Male	brain
26	chr12:105456000-105477000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:105456400-105475000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:105456600-105463800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:105456600-105475200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:105456800-105467400	Weak transcription	Fetal Stomach	stomach
31	chr12:105456800-105471200	Weak transcription	Pancreas	Pancrea
32	chr12:105456800-105476800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:105457800-105462200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:105458000-105464600	Strong transcription	NHLF	lung
35	chr12:105459000-105467200	Weak transcription	Aorta	Aorta
36	chr12:105460200-105462800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:105460200-105467000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:105460400-105462800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr12:105460400-105476600	Weak transcription	Adipose Nuclei	Adipose
40	chr12:105460400-105476600	Weak transcription	Fetal Brain Female	brain
41	chr12:105460600-105463800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:105460600-105465000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:105460600-105466200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:105460600-105476600	Weak transcription	Brain Germinal Matrix	brain
45	chr12:105460800-105462600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:105461000-105463400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:105461200-105462000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:105461200-105462000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:105461200-105462000	Genic enhancers	Osteobl	bone
50	chr12:105461200-105464000	Weak transcription	Fetal Muscle Leg	muscle

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