Variant report

Variant	rs10875770
Chromosome Location	chr12:48600520-48600521
allele	A/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	SETDB1	chr12:48600186-48601125	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
OR10AD1	TF binding region

Extended variants
information (count: 127 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10082861	0.92[JPT][hapmap]
rs1021313	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10219623	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10431526	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10437919	0.96[ASN][1000 genomes]
rs10437920	0.96[ASN][1000 genomes]
rs10467101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783234	0.87[ASN][1000 genomes]
rs10875724	0.85[JPT][hapmap]
rs10875725	0.93[JPT][hapmap]
rs10875732	0.92[JPT][hapmap]
rs10875735	0.83[CEU][hapmap]
rs10875745	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs10875746	0.84[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs10875750	0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs10875756	0.81[ASN][1000 genomes]
rs10875762	0.90[ASN][1000 genomes]
rs10875764	0.86[ASN][1000 genomes]
rs10875767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875769	0.92[ASN][1000 genomes]
rs10875772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875777	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875778	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875779	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875782	0.93[ASN][1000 genomes]
rs10875792	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875793	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168357	0.86[JPT][hapmap]
rs11168369	0.93[JPT][hapmap]
rs11168371	0.93[JPT][hapmap]
rs11168403	0.93[JPT][hapmap]
rs11168413	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs11168414	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168418	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168420	0.84[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs11168421	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs11168425	0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168427	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168433	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168450	0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11168459	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168483	0.93[ASN][1000 genomes]
rs11168487	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168493	0.88[ASN][1000 genomes]
rs11168508	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168510	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168514	0.89[ASN][1000 genomes]
rs11168516	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11558768	0.89[ASN][1000 genomes]
rs12227601	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12297470	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs12300647	0.93[ASN][1000 genomes]
rs12301339	0.89[CEU][hapmap]
rs12304476	0.93[JPT][hapmap]
rs12305182	0.86[JPT][hapmap]
rs12305511	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs12305647	0.92[ASN][1000 genomes]
rs12306451	0.93[JPT][hapmap]
rs12310813	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs12312134	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12317751	0.96[ASN][1000 genomes]
rs12318705	0.93[ASN][1000 genomes]
rs1471997	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs17122666	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs17122812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859445	0.94[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs2012773	0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2054903	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs2079295	0.86[JPT][hapmap]
rs2107638	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2171642	0.93[ASN][1000 genomes]
rs2228500	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs2269933	0.84[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap]
rs2269935	0.89[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs2269936	0.93[JPT][hapmap]
rs2279464	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2409005	0.90[ASN][1000 genomes]
rs2634675	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2732439	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2732465	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2898065	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898066	0.91[ASN][1000 genomes]
rs3185921	0.86[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs3751273	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs3782910	0.93[JPT][hapmap]
rs4760609	0.86[JPT][hapmap]
rs4760619	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4760622	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs4760625	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760681	0.89[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs4760687	0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs4760689	0.81[ASN][1000 genomes]
rs4760690	0.81[ASN][1000 genomes]
rs4760695	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs4760696	0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4760697	0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4760699	0.88[ASN][1000 genomes]
rs61940962	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941003	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61941006	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580659	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs7135779	0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs716553	0.96[ASN][1000 genomes]
rs719008	0.86[JPT][hapmap]
rs725454	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs7297298	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7299135	0.86[JPT][hapmap]
rs7299271	0.86[JPT][hapmap]
rs7302466	0.93[ASN][1000 genomes]
rs7303055	0.96[ASN][1000 genomes]
rs7486008	0.96[ASN][1000 genomes]
rs7486424	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs7975956	0.93[ASN][1000 genomes]
rs8804	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs886588	0.93[JPT][hapmap]
rs9634261	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs989144	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv976031	chr12:48594968-48610975	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv976038	chr12:48596152-48610975	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv518743	chr12:48597507-48600520	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10875770	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10875770	IRAK4	cis	parietal	SCAN
rs10875770	RND1	cis	cerebellum	SCAN
rs10875770	FAM186B	cis	parietal	SCAN
rs10875770	H1FNT	cis	cerebellum	SCAN
rs10875770	RP1-228P16.1	cis	Thyroid	GTEx
rs10875770	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs10875770	ZNF641	cis	cerebellum	SCAN
rs10875770	ASB8	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48593400-48600800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:48595600-48609600	Weak transcription	Placenta	Placenta
3	chr12:48595800-48600800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:48596600-48603800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:48597000-48606600	Weak transcription	Left Ventricle	heart
6	chr12:48597000-48606800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:48599200-48606200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:48599800-48601400	Weak transcription	Ovary	ovary
9	chr12:48600200-48600600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
10	chr12:48600200-48601200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
11	chr12:48600400-48600600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:48600400-48600600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:48600400-48601000	ZNF genes & repeats	Psoas Muscle	Psoas

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