Variant report

Variant	rs2393749
Chromosome Location	chr12:121131891-121131892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121122674..121127779-chr12:121131254..121137297,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110917	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10431384	0.80[MEX][hapmap];0.82[EUR][1000 genomes]
rs10431386	0.80[MEX][hapmap];0.83[EUR][1000 genomes]
rs11065223	0.80[ASN][1000 genomes]
rs11065231	0.91[ASN][1000 genomes]
rs11065233	0.81[ASN][1000 genomes]
rs17847	0.83[ASN][1000 genomes]
rs1814851	0.86[ASN][1000 genomes]
rs2138249	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34491494	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3794214	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3794215	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3829290	0.89[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs3914	0.86[CHD][hapmap]
rs476676	0.88[YRI][hapmap]
rs555404	0.86[CHD][hapmap]
rs658521	0.89[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs696337	0.89[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7308648	0.99[ASN][1000 genomes]
rs7964786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976497	0.89[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs7978125	0.80[AMR][1000 genomes];0.94[ASN][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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1045923	chr12:121082203-121146219	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2393749	SPPL3	cis	Adipose Subcutaneous	GTEx
rs2393749	DYNLL1	cis	cerebellum	SCAN
rs2393749	UNC119B	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121127600-121132000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr12:121127600-121132000	Weak transcription	Esophagus	oesophagus
3	chr12:121127600-121132000	Weak transcription	HSMM	muscle
4	chr12:121127600-121132600	Weak transcription	Fetal Brain Male	brain
5	chr12:121127600-121147600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:121127800-121132000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:121127800-121132000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:121127800-121132000	Weak transcription	HMEC	breast
9	chr12:121127800-121132000	Weak transcription	HSMMtube	muscle
10	chr12:121127800-121132200	Weak transcription	NH-A	brain
11	chr12:121127800-121135000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:121128600-121132600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:121128800-121132000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:121129200-121132600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:121129400-121132000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:121129400-121132000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:121129400-121132200	Weak transcription	Fetal Heart	heart
18	chr12:121130000-121132000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr12:121130000-121132000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr12:121130200-121132400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:121130200-121143000	Strong transcription	Dnd41	blood
22	chr12:121130200-121143400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:121130400-121135800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:121130400-121136200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr12:121130400-121136400	Strong transcription	Primary B cells from cord blood	blood
26	chr12:121130600-121132000	Weak transcription	Fetal Kidney	kidney
27	chr12:121130600-121132000	Weak transcription	Fetal Lung	lung
28	chr12:121130600-121132200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:121130600-121133000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr12:121130600-121136000	Genic enhancers	Fetal Intestine Large	intestine
31	chr12:121130600-121136000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:121130600-121141800	Strong transcription	NHEK	skin
33	chr12:121130600-121142000	Strong transcription	Fetal Stomach	stomach
34	chr12:121130600-121142400	Strong transcription	GM12878-XiMat	blood
35	chr12:121130600-121143200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:121130800-121132000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:121130800-121132000	Weak transcription	Small Intestine	intestine
38	chr12:121130800-121132000	Weak transcription	NHLF	lung
39	chr12:121130800-121132200	Genic enhancers	Left Ventricle	heart
40	chr12:121130800-121135600	Strong transcription	Spleen	Spleen
41	chr12:121130800-121136000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:121130800-121136000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:121130800-121140000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:121130800-121140400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:121130800-121141600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr12:121130800-121141800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:121130800-121141800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:121130800-121141800	Strong transcription	Thymus	Thymus
49	chr12:121130800-121142000	Strong transcription	Osteobl	bone
50	chr12:121130800-121142200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links