Variant report

Variant	rs11054752
Chromosome Location	chr12:12413815-12413816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12411511..12414541-chr12:12419188..12422648,4	MCF-7	breast:
2	chr12:12411626..12414518-chr12:12420226..12422396,2	K562	blood:
3	chr12:12410046..12415348-chr12:12416072..12422539,9	MCF-7	breast:
4	chr12:12413166..12415033-chr12:12416431..12418396,2	K562	blood:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10431232	0.95[EUR][1000 genomes]
rs10431303	0.94[EUR][1000 genomes]
rs10743981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1074992	0.94[EUR][1000 genomes]
rs1074993	0.94[EUR][1000 genomes]
rs10772544	0.92[EUR][1000 genomes]
rs10845498	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845504	0.94[EUR][1000 genomes]
rs10845505	0.88[EUR][1000 genomes]
rs11054701	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1181333	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1468878	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1548958	0.94[EUR][1000 genomes]
rs16907786	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16907810	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2075241	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2160521	0.83[EUR][1000 genomes]
rs2160589	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2300231	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2417090	0.92[EUR][1000 genomes]
rs3825258	0.81[EUR][1000 genomes]
rs4265667	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4494380	0.92[EUR][1000 genomes]
rs4619236	0.94[EUR][1000 genomes]
rs4763789	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61130413	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7134001	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136380	0.89[EUR][1000 genomes]
rs7295656	0.94[EUR][1000 genomes]
rs7310538	0.93[EUR][1000 genomes]
rs7311987	0.92[EUR][1000 genomes]
rs7313285	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7968660	0.93[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

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:12384800-12417200	Weak transcription	K562	blood
3	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:12390000-12416600	Weak transcription	Psoas Muscle	Psoas
5	chr12:12390800-12417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:12394200-12416800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:12394200-12417400	Weak transcription	Fetal Kidney	kidney
8	chr12:12394800-12417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:12395600-12417400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:12397600-12416600	Weak transcription	Fetal Stomach	stomach
11	chr12:12397800-12416800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:12397800-12417200	Weak transcription	Brain Anterior Caudate	brain
13	chr12:12401200-12418000	Weak transcription	Brain Substantia Nigra	brain
14	chr12:12402400-12417200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:12405000-12416600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:12405200-12416600	Weak transcription	Left Ventricle	heart
17	chr12:12405600-12417400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:12406400-12416800	Weak transcription	Hela-S3	cervix
19	chr12:12407400-12416600	Weak transcription	Fetal Brain Male	brain
20	chr12:12408200-12416800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:12408400-12416800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:12408400-12417200	Weak transcription	NHLF	lung
23	chr12:12408400-12417400	Weak transcription	NH-A	brain
24	chr12:12408400-12417400	Weak transcription	NHDF-Ad	bronchial
25	chr12:12408400-12418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:12408600-12417800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:12408800-12417200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:12409000-12416600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:12409000-12417400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:12409400-12417200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:12409600-12416600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:12409600-12416600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:12409600-12416600	Weak transcription	Ovary	ovary
34	chr12:12410000-12414400	Weak transcription	Liver	Liver
35	chr12:12410000-12416800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:12410200-12415400	Weak transcription	HepG2	liver
37	chr12:12410200-12416800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:12410200-12417000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:12410200-12417200	Weak transcription	Osteobl	bone
40	chr12:12413400-12416000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:12413400-12417400	Weak transcription	Fetal Intestine Small	intestine
42	chr12:12413600-12414200	Enhancers	A549	lung
43	chr12:12413600-12415400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:12413800-12415800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:12413800-12416800	Weak transcription	GM12878-XiMat	blood

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