Variant report

Variant	rs879493
Chromosome Location	chr6:35787417-35787418
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	chr6:35782019..35784344-chr6:35786611..35789657,3	K562	blood:
2	chr6:35773888..35775643-chr6:35786469..35788030,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10484264	0.83[GIH][hapmap]
rs1049649	0.85[CEU][hapmap];0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs10947572	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1160828	0.85[CEU][hapmap]
rs11755072	0.85[CEU][hapmap]
rs11968149	0.81[EUR][1000 genomes]
rs1326752	0.85[CEU][hapmap]
rs17653835	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs17705020	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs2038961	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038962	0.82[EUR][1000 genomes]
rs2051647	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs2301510	0.85[CEU][hapmap]
rs2395638	0.80[EUR][1000 genomes]
rs2395640	0.85[CEU][hapmap]
rs2766522	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2766527	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766528	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2817019	0.82[EUR][1000 genomes]
rs2817027	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs2859420	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3213580	0.86[CEU][hapmap]
rs3761981	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3891863	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs4340986	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs4713929	0.88[EUR][1000 genomes]
rs608267	0.82[EUR][1000 genomes]
rs612262	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs638600	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes]
rs639421	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6457858	0.82[CEU][hapmap];0.85[GIH][hapmap];0.82[EUR][1000 genomes]
rs6457859	0.81[EUR][1000 genomes]
rs6457860	0.81[EUR][1000 genomes]
rs6457862	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs651158	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs662713	0.82[CEU][hapmap]
rs677937	0.85[CEU][hapmap]
rs6908433	0.85[CEU][hapmap]
rs6909895	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6910906	0.80[EUR][1000 genomes]
rs6911849	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs6916941	0.91[CEU][hapmap]
rs6920616	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6920862	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6922695	0.81[EUR][1000 genomes]
rs6923015	0.85[CEU][hapmap];0.87[GIH][hapmap];0.81[EUR][1000 genomes]
rs6929493	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs6931888	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs6932973	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs6933241	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721694	0.80[EUR][1000 genomes]
rs7740886	0.82[CEU][hapmap];0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs7744924	0.81[EUR][1000 genomes]
rs7752545	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs7752551	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs7755022	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7755600	0.85[CEU][hapmap]
rs7758042	0.85[GIH][hapmap]
rs7774060	0.80[EUR][1000 genomes]
rs879667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296168	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs9462125	0.82[EUR][1000 genomes]
rs9462127	0.81[EUR][1000 genomes]
rs9462128	0.85[CEU][hapmap];0.84[GIH][hapmap];0.81[EUR][1000 genomes]
rs9462131	0.80[EUR][1000 genomes]
rs9462132	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs9462133	0.80[EUR][1000 genomes]
rs9462134	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9462135	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9462136	0.85[GIH][hapmap]
rs9462141	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs9462143	0.85[CEU][hapmap]
rs9470111	0.80[EUR][1000 genomes]
rs9470119	0.80[EUR][1000 genomes]
rs9470120	0.85[CEU][hapmap];0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs9470121	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9470122	0.81[EUR][1000 genomes]
rs9470123	0.81[EUR][1000 genomes]
rs9470125	0.81[EUR][1000 genomes]
rs9470126	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs9470131	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs9470134	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470136	0.80[EUR][1000 genomes]
rs9470138	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs9470139	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs9470141	0.85[CEU][hapmap]
rs9470144	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs9470147	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs9470152	0.85[CEU][hapmap]
rs9470153	0.85[CEU][hapmap]
rs9470154	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs9470155	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470156	0.84[CEU][hapmap]
rs9470162	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs9470171	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9470172	0.85[CEU][hapmap];0.83[GIH][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	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv821646	chr6:35604428-35802594	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv885802	chr6:35621781-35787417	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
6	nsv885803	chr6:35621781-35805133	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv885804	chr6:35621781-35809776	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv428143	chr6:35637083-35806504	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	esv1791730	chr6:35754783-35805144	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs879493	LHFPL5	cis	parietal	SCAN
rs879493	C6orf106	cis	cerebellum	SCAN
rs879493	SRPK1	cis	parietal	SCAN
rs879493	BRPF3	cis	cerebellum	SCAN
rs879493	SRPK1	cis	cerebellum	SCAN
rs879493	CDKN1A	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35773000-35791400	Weak transcription	Right Atrium	heart
2	chr6:35777000-35801400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:35783200-35799000	Weak transcription	Pancreas	Pancrea
4	chr6:35787200-35787800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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