Variant report

Variant	rs27574
Chromosome Location	chr5:50151965-50151966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10035164	1.00[CHB][hapmap]
rs10036060	0.82[CHB][hapmap]
rs10039639	0.90[CEU][hapmap]
rs10043477	0.85[EUR][1000 genomes]
rs10044566	1.00[CHB][hapmap]
rs10053011	0.82[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs10056836	0.82[CHB][hapmap]
rs10059085	0.82[CHB][hapmap]
rs10070517	0.81[EUR][1000 genomes]
rs10075034	0.82[CHB][hapmap]
rs10085036	0.82[CHB][hapmap]
rs10471956	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10755235	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10940472	0.88[EUR][1000 genomes]
rs10940497	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs11739828	0.87[EUR][1000 genomes]
rs11750241	0.88[EUR][1000 genomes]
rs11750771	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.88[EUR][1000 genomes]
rs12188262	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs12188654	0.80[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs12519006	0.95[EUR][1000 genomes]
rs12521579	0.95[EUR][1000 genomes]
rs13153982	0.87[EUR][1000 genomes]
rs13164951	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs13173734	0.88[EUR][1000 genomes]
rs13359044	0.95[EUR][1000 genomes]
rs1375127	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs152102	0.95[EUR][1000 genomes]
rs154133	0.95[EUR][1000 genomes]
rs154135	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs154137	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes]
rs154138	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[EUR][1000 genomes]
rs154141	0.95[EUR][1000 genomes]
rs157970	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs16884018	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs169497	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs171555	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17195388	0.95[EUR][1000 genomes]
rs182230	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs1988613	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2548581	1.00[CEU][hapmap];0.86[YRI][hapmap];0.96[EUR][1000 genomes]
rs2548582	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2548583	0.83[CEU][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs256340	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs256341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.95[EUR][1000 genomes]
rs2594706	0.82[CHB][hapmap]
rs26062	0.91[CEU][hapmap];0.82[CHB][hapmap];0.92[EUR][1000 genomes]
rs26065	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs26066	0.95[EUR][1000 genomes]
rs26068	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs26069	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[EUR][1000 genomes]
rs26071	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2697662	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs27156	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27244	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27245	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs27251	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs27254	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs27264	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs27357	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs27465	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs27466	0.82[CHB][hapmap]
rs27467	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap]
rs27468	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs27469	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes]
rs27609	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27725	0.99[EUR][1000 genomes]
rs28085	0.99[EUR][1000 genomes]
rs282549	0.95[EUR][1000 genomes]
rs282550	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes]
rs282551	0.96[EUR][1000 genomes]
rs282552	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs282553	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs282557	0.88[EUR][1000 genomes]
rs282559	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs282561	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs32376	0.82[CHB][hapmap]
rs32377	0.95[EUR][1000 genomes]
rs32378	0.95[EUR][1000 genomes]
rs32404	0.86[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]
rs32425	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes]
rs3763367	0.84[EUR][1000 genomes]
rs39613	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[EUR][1000 genomes]
rs39949	0.85[EUR][1000 genomes]
rs4029420	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs41502	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42284	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4865628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs57079776	0.81[EUR][1000 genomes]
rs578198	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs62366937	0.86[EUR][1000 genomes]
rs6450359	1.00[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs6869356	0.85[EUR][1000 genomes]
rs6872496	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs6886872	0.87[EUR][1000 genomes]
rs6890519	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs6890869	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[YRI][hapmap]
rs7449019	0.81[EUR][1000 genomes]
rs7711839	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs7723361	0.91[CEU][hapmap]
rs895801	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs921210	1.00[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs27574	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs27574	PARP8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50141400-50152400	Weak transcription	Dnd41	blood
2	chr5:50141600-50152800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:50147600-50153600	Enhancers	Primary B cells from cord blood	blood
4	chr5:50147800-50153600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:50148200-50153800	Enhancers	Primary B cells from peripheral blood	blood
6	chr5:50149600-50152400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:50149800-50152000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr5:50149800-50152200	Weak transcription	GM12878-XiMat	blood
9	chr5:50149800-50152400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:50150000-50152400	Enhancers	Adipose Nuclei	Adipose
11	chr5:50150200-50153600	Enhancers	Fetal Brain Male	brain
12	chr5:50151400-50152000	Enhancers	Fetal Stomach	stomach
13	chr5:50151400-50152200	Enhancers	Fetal Brain Female	brain
14	chr5:50151600-50153400	Enhancers	Fetal Thymus	thymus

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