Variant report

Variant	rs12047390
Chromosome Location	chr1:193338224-193338225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:193336288..193338417-chr17:39683121..39684759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171345	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10732293	0.82[CHB][hapmap]
rs10754052	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs10754055	0.81[EUR][1000 genomes]
rs10801187	0.82[CHB][hapmap]
rs10801189	0.82[CHB][hapmap]
rs10801194	0.81[EUR][1000 genomes]
rs10921323	0.82[CHB][hapmap]
rs10921325	0.86[CEU][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs10921326	0.82[CHB][hapmap]
rs10921330	0.82[CHB][hapmap]
rs10921343	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10921344	0.97[ASN][1000 genomes]
rs10921347	0.85[ASN][1000 genomes]
rs10921348	0.85[ASN][1000 genomes]
rs12025186	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025393	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12027971	0.80[ASN][1000 genomes]
rs12032958	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12033428	0.88[ASN][1000 genomes]
rs12034095	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12037055	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12037892	0.85[ASN][1000 genomes]
rs12040365	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12040832	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12041558	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12041893	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12043289	0.84[ASN][1000 genomes]
rs12043960	0.84[ASN][1000 genomes]
rs12044333	0.85[ASN][1000 genomes]
rs12048579	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12125235	1.00[ASN][1000 genomes]
rs12145954	0.99[ASN][1000 genomes]
rs1221502	0.84[EUR][1000 genomes]
rs12410213	0.81[CHB][hapmap]
rs1325197	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs1339961	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1361404	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1361405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1408830	0.82[CHB][hapmap]
rs1536098	0.82[CHB][hapmap]
rs1536099	0.82[CHB][hapmap]
rs1616234	0.81[EUR][1000 genomes]
rs1632444	0.81[EUR][1000 genomes]
rs16835282	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16835304	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16835319	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16835320	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16835338	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1749429	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1749430	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1749431	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1749432	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1769999	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1951916	0.85[ASN][1000 genomes]
rs1972345	0.84[EUR][1000 genomes]
rs2050799	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2181858	0.99[ASN][1000 genomes]
rs2182106	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs2209304	0.85[ASN][1000 genomes]
rs2254646	0.81[EUR][1000 genomes]
rs2275506	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275507	0.98[ASN][1000 genomes]
rs2477549	0.83[EUR][1000 genomes]
rs3738244	0.82[CHB][hapmap]
rs4379660	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs4403612	0.94[ASN][1000 genomes]
rs4428863	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4556337	0.85[ASN][1000 genomes]
rs4657751	0.84[ASN][1000 genomes]
rs4657848	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs4657854	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4657855	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4657856	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4657858	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs497362	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs503265	0.81[EUR][1000 genomes]
rs515964	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs543788	0.81[EUR][1000 genomes]
rs560900	0.84[EUR][1000 genomes]
rs569656	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs578639	0.84[EUR][1000 genomes]
rs58473580	0.82[ASN][1000 genomes]
rs59264807	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61082463	0.99[ASN][1000 genomes]
rs61648161	0.99[ASN][1000 genomes]
rs6428154	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs6428156	0.82[CHB][hapmap]
rs6428157	0.82[CHB][hapmap]
rs6428159	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs6428163	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6428166	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6656737	0.85[ASN][1000 genomes]
rs6665666	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs6667545	0.85[ASN][1000 genomes]
rs6671476	0.81[EUR][1000 genomes]
rs6673271	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs6675833	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs6676878	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs6680224	0.86[CEU][hapmap]
rs6686065	0.99[ASN][1000 genomes]
rs6693734	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6694727	0.88[ASN][1000 genomes]
rs6697195	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs693519	0.81[CEU][hapmap]
rs7367986	0.97[ASN][1000 genomes]
rs7417352	0.80[ASN][1000 genomes]
rs7515024	0.82[CHB][hapmap]
rs7518792	0.82[CHB][hapmap];0.81[MEX][hapmap]
rs7528595	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7534504	0.92[ASN][1000 genomes]
rs7544027	0.97[ASN][1000 genomes]
rs7550521	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7555466	0.97[ASN][1000 genomes]
rs817140	0.80[CEU][hapmap]
rs843844	0.81[CEU][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001174	chr1:193186758-193363372	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv997891	chr1:193271839-193566441	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1004003	chr1:193322299-193477254	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv535253	chr1:193322299-193477254	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3451387	chr1:193335344-193362618	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12047390	UCHL5	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193326400-193353000	Weak transcription	Fetal Lung	lung
2	chr1:193332800-193338600	Weak transcription	Aorta	Aorta
3	chr1:193337600-193338600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:193337800-193338400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr1:193337800-193338400	Active TSS	GM12878-XiMat	blood
6	chr1:193337800-193338600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:193337800-193338600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:193337800-193338600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr1:193337800-193338600	Enhancers	Small Intestine	intestine
10	chr1:193338000-193338400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:193338000-193338400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:193338000-193338400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:193338000-193338400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:193338200-193338400	Enhancers	Ovary	ovary
15	chr1:193338200-193338600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:193338200-193344200	Weak transcription	Stomach Mucosa	stomach

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