Variant report

Variant	rs3751261
Chromosome Location	chr12:12618427-12618428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12609394..12612369-chr12:12615599..12621309,5	MCF-7	breast:
2	chr12:12604694..12606790-chr12:12616651..12618443,2	MCF-7	breast:
3	chr12:12617418..12619693-chr12:12712639..12714780,2	MCF-7	breast:
4	chr12:12612821..12616513-chr12:12617624..12619681,3	K562	blood:

Variant related genes	Relation type
ENSG00000271370	Chromatin interaction
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1019340	0.83[CHB][hapmap]
rs1030069	0.89[CHB][hapmap]
rs10459098	0.83[CHB][hapmap]
rs10772566	0.83[CHB][hapmap]
rs10772567	0.82[CHB][hapmap]
rs10845539	0.83[CHB][hapmap]
rs10845544	0.81[CHB][hapmap]
rs10845545	0.83[CHB][hapmap]
rs10845551	0.94[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11054914	0.81[TSI][hapmap]
rs11609375	0.89[CHB][hapmap]
rs2160586	0.83[CHB][hapmap]
rs2216264	0.83[CHB][hapmap]
rs3925170	0.83[CHB][hapmap]
rs4763825	0.83[CHB][hapmap]
rs4763829	0.83[CHB][hapmap]
rs4763830	0.89[CHB][hapmap]
rs7132512	0.83[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7295080	0.83[CHB][hapmap]
rs7309503	0.83[CHB][hapmap]
rs7311364	0.83[CHB][hapmap]
rs7312010	0.91[ASN][1000 genomes]
rs7313825	0.89[CHB][hapmap]
rs7953025	0.83[CHB][hapmap]
rs7967111	0.83[CHB][hapmap]
rs7967466	0.83[CHB][hapmap]
rs7969849	0.83[CHB][hapmap]
rs9412	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898810	chr12:12600080-12627410	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3751261	LRP6	cis	parietal	SCAN
rs3751261	ETV6	cis	cerebellum	SCAN
rs3751261	ATF7IP	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12595200-12618600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:12596000-12620200	Weak transcription	HSMM	muscle
3	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:12596200-12620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:12599000-12618600	Weak transcription	Left Ventricle	heart
7	chr12:12601000-12620200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:12603400-12618600	Weak transcription	Pancreas	Pancrea
9	chr12:12603800-12639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:12604000-12628600	Weak transcription	Fetal Lung	lung
11	chr12:12604600-12618600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:12607800-12629400	Weak transcription	Fetal Kidney	kidney
13	chr12:12608400-12627200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:12608400-12629600	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:12609000-12623400	Weak transcription	A549	lung
16	chr12:12609200-12626800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:12609800-12628400	Weak transcription	NHLF	lung
18	chr12:12610200-12618600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:12610200-12620200	Weak transcription	Osteobl	bone
20	chr12:12610800-12622000	Weak transcription	NHEK	skin
21	chr12:12610800-12623000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:12610800-12623200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
24	chr12:12611000-12618600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:12611000-12619400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:12611000-12621600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:12611000-12627800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:12611000-12628600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:12611200-12620200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:12611200-12622000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:12611200-12627400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:12611200-12629000	Weak transcription	Hela-S3	cervix
33	chr12:12611400-12619200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:12611400-12619200	Weak transcription	Adipose Nuclei	Adipose
35	chr12:12611400-12620200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:12611400-12620200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:12611400-12620200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:12611400-12620200	Weak transcription	HSMMtube	muscle
39	chr12:12613200-12620800	Weak transcription	Brain Germinal Matrix	brain
40	chr12:12613400-12620200	Weak transcription	Brain Angular Gyrus	brain
41	chr12:12613400-12625200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:12613400-12627400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:12613800-12620600	Enhancers	Fetal Thymus	thymus
44	chr12:12614400-12620200	Weak transcription	Small Intestine	intestine
45	chr12:12614600-12622800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:12614600-12627400	Weak transcription	Spleen	Spleen
47	chr12:12614800-12622400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:12615200-12618600	Weak transcription	Right Ventricle	heart
49	chr12:12615200-12619000	Weak transcription	Aorta	Aorta
50	chr12:12615200-12619000	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links