Variant report

Variant	rs12304957
Chromosome Location	chr12:12417286-12417287
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12413166..12415033-chr12:12416431..12418396,2	K562	blood:
2	chr12:12390182..12397827-chr12:12417123..12421502,7	MCF-7	breast:
3	chr12:12410568..12413506-chr12:12416541..12418558,2	MCF-7	breast:
4	chr12:12243605..12245833-chr12:12417112..12419056,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10082834	0.81[EUR][1000 genomes]
rs10083170	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845497	0.85[EUR][1000 genomes]
rs10845499	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.83[EUR][1000 genomes]
rs11054720	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054729	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	0.89[EUR][1000 genomes]
rs12297598	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311922	0.85[EUR][1000 genomes]
rs12319942	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425185	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12427198	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448423	0.85[EUR][1000 genomes]
rs56998126	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308022	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061123	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061161	0.80[AMR][1000 genomes]
rs7957531	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.83[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	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	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12304957	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:12390800-12417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:12394200-12417400	Weak transcription	Fetal Kidney	kidney
4	chr12:12394800-12417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:12395600-12417400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:12401200-12418000	Weak transcription	Brain Substantia Nigra	brain
7	chr12:12405600-12417400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:12408400-12417400	Weak transcription	NH-A	brain
9	chr12:12408400-12417400	Weak transcription	NHDF-Ad	bronchial
10	chr12:12408400-12418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:12408600-12417800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:12409000-12417400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:12413400-12417400	Weak transcription	Fetal Intestine Small	intestine
14	chr12:12415800-12418000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:12416400-12417800	Enhancers	Colon Smooth Muscle	Colon
16	chr12:12416600-12417400	Enhancers	Ovary	ovary
17	chr12:12416600-12417600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:12416600-12417600	Enhancers	Pancreas	Pancrea
19	chr12:12416600-12417800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:12416600-12417800	Enhancers	Fetal Brain Male	brain
21	chr12:12416600-12417800	Enhancers	Fetal Muscle Leg	muscle
22	chr12:12416600-12417800	Enhancers	Fetal Stomach	stomach
23	chr12:12416600-12417800	Enhancers	Left Ventricle	heart
24	chr12:12416600-12417800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr12:12416600-12417800	Enhancers	Stomach Mucosa	stomach
26	chr12:12416600-12418000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:12416600-12418200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:12416600-12418200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:12416600-12418200	Flanking Active TSS	Liver	Liver
30	chr12:12416600-12418200	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:12416600-12418200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:12416800-12417400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:12416800-12417400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr12:12416800-12417400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:12416800-12417400	Enhancers	Fetal Heart	heart
36	chr12:12416800-12417400	Weak transcription	Psoas Muscle	Psoas
37	chr12:12416800-12417400	Enhancers	Stomach Smooth Muscle	stomach
38	chr12:12416800-12417600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:12416800-12417600	Enhancers	HMEC	breast
40	chr12:12416800-12417800	Enhancers	Adipose Nuclei	Adipose
41	chr12:12416800-12417800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr12:12416800-12418000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:12416800-12418200	Flanking Active TSS	Fetal Brain Female	brain
44	chr12:12416800-12418400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr12:12416800-12420600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:12416800-12420600	Active TSS	GM12878-XiMat	blood
47	chr12:12417000-12417600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
48	chr12:12417000-12417600	Active TSS	Lung	lung
49	chr12:12417000-12417600	Flanking Active TSS	HepG2	liver
50	chr12:12417000-12417800	Weak transcription	Right Atrium	heart

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