Variant report

Variant	rs16878863
Chromosome Location	chr6:87983065-87983066
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	chr6:87982117..87985714-chr6:87986469..87990458,4	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10488045	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs10498960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878473	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs16878570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs16878622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs16878638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs16878712	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878713	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs16878729	0.91[EUR][1000 genomes]
rs16878734	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878736	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878809	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878856	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878942	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878991	0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs16878999	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs16879012	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs1925693	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs41273281	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41273283	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41397850	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs41398947	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs55647962	0.85[EUR][1000 genomes]
rs56010354	0.82[AFR][1000 genomes]
rs56193950	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56305030	0.94[AFR][1000 genomes]
rs56678817	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56743579	0.88[EUR][1000 genomes]
rs56847789	0.85[EUR][1000 genomes]
rs56999910	0.88[EUR][1000 genomes]
rs57043501	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57116567	0.88[EUR][1000 genomes]
rs57217108	0.88[EUR][1000 genomes]
rs57421283	0.94[EUR][1000 genomes]
rs57552196	0.94[AFR][1000 genomes]
rs57607342	0.88[EUR][1000 genomes]
rs57631457	0.81[AFR][1000 genomes]
rs57962992	0.85[EUR][1000 genomes]
rs58269367	0.94[EUR][1000 genomes]
rs58327183	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58474842	0.94[EUR][1000 genomes]
rs58731649	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58735749	0.94[EUR][1000 genomes]
rs58751410	0.85[EUR][1000 genomes]
rs59127357	0.82[AFR][1000 genomes]
rs59138817	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59150116	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59214037	0.94[EUR][1000 genomes]
rs59495279	0.88[EUR][1000 genomes]
rs59597706	0.89[AFR][1000 genomes]
rs59654654	0.87[EUR][1000 genomes]
rs59875769	0.94[EUR][1000 genomes]
rs60074363	0.94[EUR][1000 genomes]
rs60285195	0.94[EUR][1000 genomes]
rs60544317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60628059	0.86[AFR][1000 genomes]
rs60845773	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60985818	0.81[EUR][1000 genomes]
rs60994855	0.85[EUR][1000 genomes]
rs61047847	0.88[EUR][1000 genomes]
rs61174011	0.89[AFR][1000 genomes]
rs61379368	0.94[EUR][1000 genomes]
rs61705669	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483720	0.94[EUR][1000 genomes]
rs73483728	0.94[EUR][1000 genomes]
rs73483743	0.94[EUR][1000 genomes]
rs73483749	0.94[EUR][1000 genomes]
rs73483752	0.94[EUR][1000 genomes]
rs73483758	0.94[EUR][1000 genomes]
rs73483760	0.94[EUR][1000 genomes]
rs73483765	0.94[EUR][1000 genomes]
rs73483769	0.94[EUR][1000 genomes]
rs73483771	0.91[EUR][1000 genomes]
rs73483774	0.94[EUR][1000 genomes]
rs73483790	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73483796	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73483799	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485808	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485811	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485813	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485815	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485820	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485826	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485828	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485848	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485849	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73499800	0.88[EUR][1000 genomes]
rs73499802	0.88[EUR][1000 genomes]
rs73501611	0.85[EUR][1000 genomes]
rs73501620	0.88[EUR][1000 genomes]
rs73501623	0.88[EUR][1000 genomes]
rs73501629	0.88[EUR][1000 genomes]
rs73501632	0.88[EUR][1000 genomes]
rs73501636	0.88[EUR][1000 genomes]
rs73501638	0.88[EUR][1000 genomes]
rs73501641	0.88[EUR][1000 genomes]
rs73501658	0.88[EUR][1000 genomes]
rs73501662	0.88[EUR][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	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2752763	chr6:87981595-88001064	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16878863	SEMA5A	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87966400-87989200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:87967800-87989000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr6:87968200-87991200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:87968400-87984400	Weak transcription	NHDF-Ad	bronchial
5	chr6:87968600-87984200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:87970000-87984600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:87970200-87984600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:87970400-87984400	Weak transcription	NH-A	brain
9	chr6:87970600-87983400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:87970600-87984200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:87970600-87988800	Weak transcription	Fetal Thymus	thymus
12	chr6:87970600-87994800	Weak transcription	Fetal Brain Female	brain
13	chr6:87971200-87985800	Weak transcription	Brain Germinal Matrix	brain
14	chr6:87975000-87984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links