Variant report

Variant	rs10875736
Chromosome Location	chr12:48472366-48472367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48468062..48470836-chr12:48471643..48474168,2	K562	blood:
2	chr12:48471151..48472843-chr12:48551945..48554852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258051	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10219623	0.82[AMR][1000 genomes]
rs10875730	0.81[AFR][1000 genomes]
rs10875731	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10875732	0.81[AFR][1000 genomes]
rs10875735	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875737	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875738	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875740	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875745	0.82[AMR][1000 genomes]
rs10875746	0.82[EUR][1000 genomes]
rs10875747	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875748	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875750	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10875756	0.82[EUR][1000 genomes]
rs11168369	0.81[AFR][1000 genomes]
rs11168374	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11168383	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168386	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168401	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168403	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168413	0.82[AMR][1000 genomes]
rs11168414	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168418	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11168420	0.91[EUR][1000 genomes]
rs11168422	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11168427	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168433	0.82[EUR][1000 genomes]
rs12296244	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12297004	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12297470	0.82[AMR][1000 genomes]
rs12301339	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12304476	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12306451	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12310813	0.82[AMR][1000 genomes]
rs12310999	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12311774	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12311953	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12313300	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12313404	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12315625	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17122620	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17122666	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1859445	0.82[AMR][1000 genomes]
rs2107638	0.82[AMR][1000 genomes]
rs2158516	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2228500	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2269935	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2269936	0.81[AFR][1000 genomes]
rs2286021	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3782910	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782911	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760680	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760681	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4760689	0.82[EUR][1000 genomes]
rs4760690	0.82[EUR][1000 genomes]
rs58952582	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60761335	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61918774	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs61918806	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61918809	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61918810	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs725454	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73102065	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73102067	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7485355	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8804	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs886588	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs989144	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10875736	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs10875736	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs10875736	RP1-228P16.1	cis	Thyroid	GTEx
rs10875736	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10875736	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
3	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
5	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:48444200-48474600	Weak transcription	Gastric	stomach
7	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:48453800-48474800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:48454600-48478800	Weak transcription	Pancreas	Pancrea
11	chr12:48457400-48482000	Weak transcription	Right Ventricle	heart
12	chr12:48457600-48478600	Weak transcription	HSMMtube	muscle
13	chr12:48459200-48479000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:48463600-48476200	Weak transcription	HUVEC	blood vessel
15	chr12:48464400-48476200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:48464600-48472600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:48464600-48489400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:48464800-48476000	Weak transcription	Fetal Brain Male	brain
19	chr12:48464800-48482400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:48465000-48474000	Weak transcription	Lung	lung
21	chr12:48465000-48474600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:48465000-48477000	Weak transcription	Brain Angular Gyrus	brain
23	chr12:48465000-48478800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:48465000-48478800	Weak transcription	Aorta	Aorta
25	chr12:48465000-48487400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:48465800-48476800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:48466200-48481400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:48466400-48472600	Weak transcription	Ovary	ovary
29	chr12:48466800-48472600	Weak transcription	Fetal Intestine Small	intestine
30	chr12:48466800-48472600	Weak transcription	Fetal Stomach	stomach
31	chr12:48466800-48478800	Weak transcription	Esophagus	oesophagus
32	chr12:48468200-48472400	Weak transcription	NHLF	lung
33	chr12:48468200-48472600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:48468200-48472600	Weak transcription	Hela-S3	cervix
35	chr12:48468200-48476000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:48468200-48476000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:48468200-48476000	Weak transcription	HSMM	muscle
38	chr12:48468200-48478800	Weak transcription	HepG2	liver
39	chr12:48468400-48472600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:48468400-48472600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:48468400-48474000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:48468400-48474000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:48468400-48474200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:48468400-48474200	Weak transcription	Spleen	Spleen
45	chr12:48468400-48474600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:48468400-48474600	Weak transcription	GM12878-XiMat	blood
47	chr12:48468400-48476000	Weak transcription	Fetal Lung	lung
48	chr12:48468400-48476200	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:48468400-48476400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr12:48468400-48478600	Weak transcription	Colonic Mucosa	Colon

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