Variant report

Variant	rs10039617
Chromosome Location	chr5:43319352-43319353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43317902..43322981-chr5:43481310..43485005,5	K562	blood:
2	chr5:43310462..43313861-chr5:43318500..43321089,4	K562	blood:
3	chr5:43312195..43313861-chr5:43318989..43321314,3	K562	blood:

Variant related genes	Relation type
ENSG00000151881	Chromatin interaction
ENSG00000112972	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs10039048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10462048	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs10512825	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs10512827	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10512828	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs10805671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10805672	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs10805673	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10805674	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10805675	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs10941620	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10941621	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs10941622	0.90[EUR][1000 genomes]
rs10941623	0.90[EUR][1000 genomes]
rs10941628	0.91[EUR][1000 genomes]
rs10941630	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs10941631	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10941632	0.83[EUR][1000 genomes]
rs11738086	0.88[EUR][1000 genomes]
rs11739009	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs11739665	0.90[EUR][1000 genomes]
rs11740128	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11741246	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs11742171	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs11742712	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs11743622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11743633	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11746629	0.81[EUR][1000 genomes]
rs11747105	0.91[EUR][1000 genomes]
rs11747834	0.91[EUR][1000 genomes]
rs11950040	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11950448	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs11951584	0.88[EUR][1000 genomes]
rs11956635	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs11956936	0.84[EUR][1000 genomes]
rs11956988	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs11960415	0.83[EUR][1000 genomes]
rs12109933	0.84[EUR][1000 genomes]
rs12189016	0.91[EUR][1000 genomes]
rs12189447	0.88[EUR][1000 genomes]
rs12513864	0.82[EUR][1000 genomes]
rs12514393	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12514399	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12515072	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs12516435	0.87[EUR][1000 genomes]
rs12517362	0.86[EUR][1000 genomes]
rs12518032	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs12518127	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs12519554	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12520012	0.90[EUR][1000 genomes]
rs12520895	0.83[EUR][1000 genomes]
rs12522178	0.87[EUR][1000 genomes]
rs13161494	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13187876	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13659	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs1545753	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs1548097	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1564196	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1564197	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs1564198	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244818	0.92[CEU][hapmap]
rs2086133	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2126947	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2126948	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs2126949	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2169781	0.91[EUR][1000 genomes]
rs2330150	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2330242	0.85[EUR][1000 genomes]
rs2330243	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35231094	0.81[EUR][1000 genomes]
rs35239179	0.90[EUR][1000 genomes]
rs3733768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733769	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs4050485	0.88[EUR][1000 genomes]
rs4254917	0.82[AMR][1000 genomes]
rs4288122	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs4320264	0.88[EUR][1000 genomes]
rs4373285	0.90[EUR][1000 genomes]
rs4395639	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4443425	0.83[EUR][1000 genomes]
rs4443426	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs4574553	0.88[EUR][1000 genomes]
rs4591755	0.91[EUR][1000 genomes]
rs4866734	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4866737	0.92[EUR][1000 genomes]
rs4866738	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs4866741	0.96[CEU][hapmap];0.93[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4866813	0.90[EUR][1000 genomes]
rs4866818	0.92[CEU][hapmap]
rs4866820	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs4866821	0.88[EUR][1000 genomes]
rs4866822	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4866824	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4866825	0.87[EUR][1000 genomes]
rs4866826	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55634155	0.92[EUR][1000 genomes]
rs55647314	0.83[EUR][1000 genomes]
rs55759097	0.82[EUR][1000 genomes]
rs55759722	0.87[EUR][1000 genomes]
rs55794239	0.89[EUR][1000 genomes]
rs55800451	0.85[EUR][1000 genomes]
rs55992392	0.87[EUR][1000 genomes]
rs56023994	0.84[EUR][1000 genomes]
rs56029402	0.85[EUR][1000 genomes]
rs56071328	0.87[EUR][1000 genomes]
rs56114604	0.90[EUR][1000 genomes]
rs56185290	0.88[EUR][1000 genomes]
rs56206275	0.88[EUR][1000 genomes]
rs57066570	0.87[EUR][1000 genomes]
rs57392430	0.85[EUR][1000 genomes]
rs57401732	0.92[EUR][1000 genomes]
rs58358642	0.87[EUR][1000 genomes]
rs58679159	0.92[EUR][1000 genomes]
rs58966636	0.87[EUR][1000 genomes]
rs59078439	0.88[EUR][1000 genomes]
rs59625262	0.87[EUR][1000 genomes]
rs59814709	0.88[EUR][1000 genomes]
rs60207549	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60445501	0.92[EUR][1000 genomes]
rs61627503	0.86[EUR][1000 genomes]
rs6451684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66585077	0.81[EUR][1000 genomes]
rs66691321	0.90[EUR][1000 genomes]
rs66914803	0.92[EUR][1000 genomes]
rs67415672	0.85[EUR][1000 genomes]
rs67497876	0.91[EUR][1000 genomes]
rs67620667	0.85[EUR][1000 genomes]
rs67651757	0.91[EUR][1000 genomes]
rs67817333	0.91[EUR][1000 genomes]
rs6814	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs6863246	0.88[EUR][1000 genomes]
rs6863360	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867954	0.83[EUR][1000 genomes]
rs6886499	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6887351	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6895805	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6898398	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7445066	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs754527	0.87[CHB][hapmap]
rs7701391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701642	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs7704588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7708779	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs7714027	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs7714919	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7716091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7720165	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs7720681	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7722781	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7727047	0.85[CEU][hapmap]
rs7734293	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs9292871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292874	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9790987	0.93[CEU][hapmap];0.90[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	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv3360596	chr5:43315646-43336665	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10039617	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43315600-43319600	Weak transcription	K562	blood
2	chr5:43319200-43319600	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links