Variant report

Variant	rs10514906
Chromosome Location	chr5:60474581-60474582
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:60472131..60474051-chr5:60474315..60476494,2	K562	blood:
2	chr5:60468797..60470812-chr5:60474024..60476089,2	MCF-7	breast:
3	chr5:60473247..60475039-chr5:60548494..60550640,2	MCF-7	breast:
4	chr5:60472151..60475021-chr5:60626975..60629740,3	K562	blood:
5	chr5:60474350..60475293-chr5:60600116..60600975,7	MCF-7	breast:
6	chr5:60474401..60475293-chr5:60600199..60600951,3	MCF-7	breast:
7	chr5:60473979..60476884-chr5:60480404..60482643,2	MCF-7	breast:
8	chr5:60473013..60474632-chr5:60628436..60631352,3	MCF-7	breast:
9	chr5:60454738..60463245-chr5:60465333..60477980,25	K562	blood:
10	chr5:60472733..60477448-chr5:60625158..60628299,7	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDUFAF2-2	chr5:60474133-60476024	NONHSAT101661

No data

Variant related genes	Relation type
ENSG00000251279	Chromatin interaction
ENSG00000130449	Chromatin interaction
ENSG00000249279	Chromatin interaction
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 153 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs10471502	0.88[ASN][1000 genomes]
rs11957772	0.88[ASN][1000 genomes]
rs124898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12518865	0.88[ASN][1000 genomes]
rs13168191	0.88[ASN][1000 genomes]
rs1382914	0.88[ASN][1000 genomes]
rs158564	0.88[ASN][1000 genomes]
rs158570	0.91[ASN][1000 genomes]
rs158571	0.86[ASN][1000 genomes]
rs158696	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158697	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158699	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158700	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158914	0.86[ASN][1000 genomes]
rs158915	0.86[ASN][1000 genomes]
rs158918	0.91[ASN][1000 genomes]
rs158919	0.86[ASN][1000 genomes]
rs158922	0.86[ASN][1000 genomes]
rs158923	0.88[ASN][1000 genomes]
rs158924	0.88[ASN][1000 genomes]
rs158927	0.91[ASN][1000 genomes]
rs158929	0.91[ASN][1000 genomes]
rs158931	0.86[ASN][1000 genomes]
rs158932	0.83[ASN][1000 genomes]
rs158933	0.86[ASN][1000 genomes]
rs158934	0.86[ASN][1000 genomes]
rs158935	0.86[ASN][1000 genomes]
rs158936	0.86[ASN][1000 genomes]
rs158937	0.91[ASN][1000 genomes]
rs158938	0.86[ASN][1000 genomes]
rs159357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs159358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs159371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs159374	0.94[ASN][1000 genomes]
rs159375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs159376	0.94[ASN][1000 genomes]
rs159377	0.94[ASN][1000 genomes]
rs159378	0.94[ASN][1000 genomes]
rs159380	0.94[ASN][1000 genomes]
rs162228	0.91[ASN][1000 genomes]
rs162234	0.88[ASN][1000 genomes]
rs162238	0.88[ASN][1000 genomes]
rs162241	0.88[ASN][1000 genomes]
rs162242	0.88[ASN][1000 genomes]
rs162243	0.91[ASN][1000 genomes]
rs162244	0.88[ASN][1000 genomes]
rs162246	0.91[ASN][1000 genomes]
rs162248	0.88[ASN][1000 genomes]
rs162251	0.88[ASN][1000 genomes]
rs168710	0.88[ASN][1000 genomes]
rs16878547	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16878548	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs169700	0.88[ASN][1000 genomes]
rs172348	0.88[ASN][1000 genomes]
rs172945	0.88[ASN][1000 genomes]
rs1820082	0.91[ASN][1000 genomes]
rs182410	0.94[ASN][1000 genomes]
rs187459	0.88[ASN][1000 genomes]
rs1989653	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2080869	0.88[ASN][1000 genomes]
rs2263514	0.88[ASN][1000 genomes]
rs2270822	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248677	0.88[ASN][1000 genomes]
rs248682	0.88[ASN][1000 genomes]
rs248683	0.88[ASN][1000 genomes]
rs248685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs248688	0.88[ASN][1000 genomes]
rs2545475	0.94[ASN][1000 genomes]
rs2545478	0.89[ASN][1000 genomes]
rs2545493	0.91[ASN][1000 genomes]
rs2545503	0.94[ASN][1000 genomes]
rs256375	0.94[ASN][1000 genomes]
rs256376	0.94[ASN][1000 genomes]
rs2619890	0.88[ASN][1000 genomes]
rs2619893	0.88[ASN][1000 genomes]
rs2650512	0.88[ASN][1000 genomes]
rs2650517	0.88[ASN][1000 genomes]
rs2694518	0.91[ASN][1000 genomes]
rs2694528	0.94[ASN][1000 genomes]
rs2694530	0.88[ASN][1000 genomes]
rs2694531	0.88[ASN][1000 genomes]
rs290503	0.88[ASN][1000 genomes]
rs290506	0.88[ASN][1000 genomes]
rs290507	0.88[ASN][1000 genomes]
rs290511	0.94[ASN][1000 genomes]
rs290513	0.88[ASN][1000 genomes]
rs290514	0.91[ASN][1000 genomes]
rs290515	0.91[ASN][1000 genomes]
rs2950235	0.88[ASN][1000 genomes]
rs295522	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs295524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs295531	0.94[ASN][1000 genomes]
rs295533	0.88[ASN][1000 genomes]
rs295551	0.94[ASN][1000 genomes]
rs295559	0.94[ASN][1000 genomes]
rs295560	0.94[ASN][1000 genomes]
rs295561	0.94[ASN][1000 genomes]
rs295563	0.94[ASN][1000 genomes]
rs295564	0.94[ASN][1000 genomes]
rs295566	0.91[ASN][1000 genomes]
rs295569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs295573	0.94[ASN][1000 genomes]
rs295578	0.94[ASN][1000 genomes]
rs295579	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3101879	0.88[ASN][1000 genomes]
rs3108388	0.88[ASN][1000 genomes]
rs329622	0.88[ASN][1000 genomes]
rs329623	0.88[ASN][1000 genomes]
rs329624	0.88[ASN][1000 genomes]
rs329625	0.88[ASN][1000 genomes]
rs329626	0.88[ASN][1000 genomes]
rs34591	0.88[ASN][1000 genomes]
rs34592	0.88[ASN][1000 genomes]
rs34593	0.88[ASN][1000 genomes]
rs34610	0.94[ASN][1000 genomes]
rs34614	0.94[ASN][1000 genomes]
rs34621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34624	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs34636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34637	0.94[ASN][1000 genomes]
rs34638	0.88[ASN][1000 genomes]
rs34639	0.88[ASN][1000 genomes]
rs34643	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs39661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs40084	0.88[ASN][1000 genomes]
rs40421	0.88[ASN][1000 genomes]
rs4141502	0.88[ASN][1000 genomes]
rs42437	0.88[ASN][1000 genomes]
rs4699967	0.88[ASN][1000 genomes]
rs4700406	0.88[ASN][1000 genomes]
rs4700410	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56409036	0.88[ASN][1000 genomes]
rs59292447	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862622	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868884	0.88[ASN][1000 genomes]
rs6869073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6869454	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878124	0.88[ASN][1000 genomes]
rs6886481	0.88[ASN][1000 genomes]
rs6893210	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723276	0.88[ASN][1000 genomes]
rs7712364	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718028	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723754	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs810883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs810884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9291702	0.86[EUR][1000 genomes];0.94[ASN][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	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60460400-60475000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60468600-60484400	Weak transcription	Aorta	Aorta
3	chr5:60472800-60476600	Weak transcription	Right Atrium	heart
4	chr5:60473800-60476600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:60474200-60476600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr5:60474200-60476800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr5:60474400-60476600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links