Variant report

Variant	rs10861343
Chromosome Location	chr12:105462978-105462979
allele	G/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	POLR2A	chr12:105462832-105463032	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:105392063..105394759-chr12:105462525..105464694,2	K562	blood:
2	chr12:105462061..105464971-chr12:105467653..105470176,2	K562	blood:
3	chr12:105461590..105464324-chr12:105467653..105469817,3	K562	blood:
4	chr12:105461700..105464366-chr12:105466158..105469236,3	MCF-7	breast:

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

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10459203	0.90[YRI][hapmap]
rs10861345	0.95[CEU][hapmap]
rs11112358	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112361	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs11614837	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs1196845	0.81[CEU][hapmap]
rs12310047	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1345094	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2374450	0.96[EUR][1000 genomes]
rs6539185	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539191	0.96[EUR][1000 genomes]
rs7298218	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7962796	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935247	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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

No data

Chromatin state (count:57 , 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	chr12:105447200-105466800	Weak transcription	Brain Angular Gyrus	brain
13	chr12:105447200-105477200	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:105449400-105476800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:105450800-105468200	Weak transcription	Brain Anterior Caudate	brain
16	chr12:105452000-105464200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:105452000-105466200	Weak transcription	GM12878-XiMat	blood
18	chr12:105453400-105476800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:105454200-105476600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:105455600-105465200	Strong transcription	HMEC	breast
21	chr12:105455600-105467800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:105455600-105476400	Weak transcription	Fetal Brain Male	brain
23	chr12:105456000-105477000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:105456400-105475000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:105456600-105463800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:105456600-105475200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:105456800-105467400	Weak transcription	Fetal Stomach	stomach
28	chr12:105456800-105471200	Weak transcription	Pancreas	Pancrea
29	chr12:105456800-105476800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:105458000-105464600	Strong transcription	NHLF	lung
31	chr12:105459000-105467200	Weak transcription	Aorta	Aorta
32	chr12:105460200-105467000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:105460400-105476600	Weak transcription	Adipose Nuclei	Adipose
34	chr12:105460400-105476600	Weak transcription	Fetal Brain Female	brain
35	chr12:105460600-105463800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:105460600-105465000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:105460600-105466200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:105460600-105476600	Weak transcription	Brain Germinal Matrix	brain
39	chr12:105461000-105463400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:105461200-105464000	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:105461400-105465200	Strong transcription	NHDF-Ad	bronchial
42	chr12:105461800-105463800	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr12:105461800-105464000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:105461800-105464600	Strong transcription	NH-A	brain
45	chr12:105461800-105468000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:105462000-105463200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:105462000-105463400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:105462000-105463400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:105462000-105467800	Strong transcription	Osteobl	bone
50	chr12:105462200-105463000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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