Variant report

Variant	rs486463
Chromosome Location	chr1:59036141-59036142
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59035270..59037403-chr1:59084300..59086299,2	MCF-7	breast:
2	chr1:59032420..59036590-chr1:59038071..59040162,4	K562	blood:
3	chr1:59034065..59036590-chr1:59038071..59040103,2	K562	blood:
4	chr1:59033300..59036238-chr1:59156402..59159118,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10458559	0.95[CEU][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10789064	0.95[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10789065	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10789066	0.95[CEU][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10789067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889098	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889100	0.95[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10889101	0.84[CEU][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1109895	0.90[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1109896	0.94[CEU][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207237	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11207250	1.00[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207251	0.95[CEU][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207252	0.95[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207253	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207254	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11581395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs12030713	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12124662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs12125391	0.95[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12142098	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1388981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1775002	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2087799	0.95[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232822	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232827	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232830	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232841	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232842	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs232844	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232847	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232848	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232849	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2406784	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3087585	0.95[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs338225	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs3551	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4912195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs4912344	0.85[ASN][1000 genomes]
rs525929	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs562166	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs584579	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs602579	0.94[ASW][hapmap];0.95[CEU][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs603031	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61779295	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61779296	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs620342	0.95[CEU][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs627218	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6587820	0.95[CEU][hapmap]
rs6587828	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs659061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6656025	0.88[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap]
rs6667614	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs6667703	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6687324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs672359	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67639631	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7355165	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7355166	0.83[EUR][1000 genomes]
rs7517424	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7520008	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7536230	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs7544032	0.85[ASN][1000 genomes]
rs7546900	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7547036	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs905567	0.95[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9660901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs486463	OMA1	cis	multi-tissue	Pritchard
rs486463	MYSM1	cis	parietal	SCAN
rs486463	TACSTD2	cis	Whole Blood	GTEx
rs486463	TACSTD2	cis	Thyroid	GTEx
rs486463	OMA1	cis	lymphoblastoid	seeQTL
rs486463	DAB1	cis	parietal	SCAN
rs486463	DAB1	cis	cerebellum	SCAN
rs486463	OMA1	cis	cerebellum	SCAN
rs486463	OMA1	cis	parietal	SCAN
rs486463	TACSTD2	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59033800-59039800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:59034200-59036200	Enhancers	GM12878-XiMat	blood
3	chr1:59034400-59037400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:59034400-59039400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:59034600-59039000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:59034600-59039800	Enhancers	Stomach Mucosa	stomach
7	chr1:59034800-59038400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:59035000-59038200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:59035000-59038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:59035000-59039800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:59035200-59037000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:59035400-59037400	Weak transcription	NHEK	skin
13	chr1:59035800-59036400	Enhancers	HepG2	liver
14	chr1:59035800-59037200	Enhancers	Brain Angular Gyrus	brain
15	chr1:59035800-59037400	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:59035800-59037800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr1:59035800-59038400	Enhancers	HMEC	breast
18	chr1:59035800-59041000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr1:59036000-59036200	Enhancers	Esophagus	oesophagus
20	chr1:59036000-59036200	Enhancers	Pancreas	Pancrea
21	chr1:59036000-59036600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:59036000-59036800	Enhancers	Placenta	Placenta
23	chr1:59036000-59037800	Enhancers	Brain Hippocampus Middle	brain
24	chr1:59036000-59038000	Enhancers	Brain Substantia Nigra	brain

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