Variant report

Variant	rs12916980
Chromosome Location	chr15:83306447-83306448
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83296467..83300526-chr15:83302412..83306697,6	K562	blood:
2	chr15:83304208..83306459-chr15:83417486..83420687,3	K562	blood:
3	chr15:83238728..83241001-chr15:83305797..83309548,3	K562	blood:

Variant related genes	Relation type
ENSG00000214575	Chromatin interaction
ENSG00000250988	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10400906	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10468217	0.92[ASN][1000 genomes]
rs10906984	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1145172	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1145173	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs11631963	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11633829	0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11635624	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs11637433	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11855735	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148332	0.94[ASN][1000 genomes]
rs12438312	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12442686	0.93[ASN][1000 genomes]
rs1259180	0.92[ASN][1000 genomes]
rs1259182	0.97[ASN][1000 genomes]
rs1259183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267657	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1267658	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1267659	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1269134	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911134	0.92[ASN][1000 genomes]
rs1313492	0.96[ASN][1000 genomes]
rs1313493	0.96[ASN][1000 genomes]
rs1367841	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1594511	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17158390	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864699	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2099259	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278355	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs2567635	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2567636	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.94[ASN][1000 genomes]
rs2678445	0.88[ASN][1000 genomes]
rs2678448	0.94[ASN][1000 genomes]
rs28374463	0.95[ASN][1000 genomes]
rs28415133	0.93[ASN][1000 genomes]
rs28667458	0.92[ASN][1000 genomes]
rs2870965	0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2870966	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28808991	0.95[ASN][1000 genomes]
rs34186444	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35934048	0.90[ASN][1000 genomes]
rs36109438	0.93[ASN][1000 genomes]
rs3970696	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4778686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779032	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4779039	0.96[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4779041	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4779044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4779050	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4779053	0.92[ASN][1000 genomes]
rs4779054	0.83[ASN][1000 genomes]
rs55924160	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57181760	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6603033	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs698500	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7165125	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7166248	0.92[ASN][1000 genomes]
rs7167880	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7171180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7178350	0.96[ASN][1000 genomes]
rs7181761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7182403	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7183881	0.99[ASN][1000 genomes]
rs7494860	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7496954	0.99[ASN][1000 genomes]
rs783520	0.98[ASN][1000 genomes]
rs783521	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs783522	0.99[ASN][1000 genomes]
rs783523	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs783525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs783526	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs783527	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs783529	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs783530	0.94[ASN][1000 genomes]
rs783531	0.93[ASN][1000 genomes]
rs783532	0.94[ASN][1000 genomes]
rs783533	0.96[ASN][1000 genomes]
rs783534	0.96[ASN][1000 genomes]
rs783535	0.93[ASN][1000 genomes]
rs783536	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs783537	0.92[ASN][1000 genomes]
rs783539	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs783540	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs783543	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs783545	0.92[ASN][1000 genomes]
rs803687	0.86[ASN][1000 genomes]
rs803688	0.87[ASN][1000 genomes]
rs803747	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[ASN][1000 genomes]
rs8040293	0.96[ASN][1000 genomes]
rs8043401	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9652567	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427965	chr15:82741381-83310525	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv428309	chr15:82741381-83310525	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv2758391	chr15:82879646-83310525	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	esv2760046	chr15:82879646-83310525	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1035899	chr15:83108446-83315731	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833071	chr15:83123646-83310510	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	esv3344877	chr15:83294946-83316565	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
15	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
16	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
17	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12916980	RP13-996F3.5	cis	Esophagus Mucosa	GTEx
rs12916980	GOLGA6L10	cis	Esophagus Mucosa	GTEx
rs12916980	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL
rs12916980	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs12916980	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL
rs12916980	GOLGA6L10	cis	Esophagus Muscularis	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83282800-83312800	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:83305800-83307600	Weak transcription	K562	blood
3	chr15:83306400-83315000	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links