Variant report

Variant	rs10875715
Chromosome Location	chr12:48381756-48381757
allele	C/G
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	MAX	chr12:48381486-48381807	K562	blood:	n/a	n/a
2	EGR1	chr12:48381540-48381819	K562	blood:	n/a	n/a
3	ZNF263	chr12:48381559-48381922	HEK293-T-REx	kidney:	n/a	chr12:48381692-48381713
4	MXI1	chr12:48381265-48381966	IMR90	lung:	n/a	n/a
5	POLR2A	chr12:48381507-48381922	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
COL2A1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10875714	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12228854	0.86[EUR][1000 genomes]
rs12308909	0.88[EUR][1000 genomes]
rs2213163	0.92[EUR][1000 genomes]
rs2898056	0.86[EUR][1000 genomes]
rs3737548	0.92[EUR][1000 genomes]
rs3782915	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809322	0.86[EUR][1000 genomes]
rs3809324	0.86[EUR][1000 genomes]
rs56037230	0.92[EUR][1000 genomes]
rs56959315	0.92[EUR][1000 genomes]
rs740022	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10875715	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10875715	RP1-228P16.1	cis	Thyroid	GTEx
rs10875715	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs10875715	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
3	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
4	chr12:48379400-48382000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:48381000-48383600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:48381200-48381800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:48381200-48382000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:48381200-48382600	Enhancers	Fetal Brain Male	brain
9	chr12:48381200-48385400	Enhancers	Fetal Muscle Leg	muscle
10	chr12:48381200-48385800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:48381400-48381800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:48381400-48381800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr12:48381400-48382400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:48381400-48382600	Bivalent Enhancer	Fetal Stomach	stomach
15	chr12:48381400-48383800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:48381400-48384400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:48381400-48386400	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:48381400-48386800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:48381400-48388800	Weak transcription	Fetal Intestine Small	intestine
20	chr12:48381600-48381800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:48381600-48381800	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:48381600-48381800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:48381600-48381800	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:48381600-48381800	Enhancers	Fetal Kidney	kidney
25	chr12:48381600-48381800	Enhancers	Fetal Thymus	thymus
26	chr12:48381600-48382000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:48381600-48382000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr12:48381600-48382000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
29	chr12:48381600-48382200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:48381600-48382200	Bivalent Enhancer	Fetal Lung	lung
31	chr12:48381600-48382200	Enhancers	Right Atrium	heart
32	chr12:48381600-48382600	Enhancers	Fetal Brain Female	brain
33	chr12:48381600-48383000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
34	chr12:48381600-48383200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:48381600-48383200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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