Variant report

Variant	rs478088
Chromosome Location	chr18:12379183-12379184
allele	G/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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12377168..12379207-chr18:12397711..12400933,3	K562	blood:
2	chr18:12375314..12379217-chr18:12700733..12704866,11	K562	blood:
3	chr18:12376943..12379295-chr18:12946308..12947818,2	K562	blood:
4	chr18:12375309..12380137-chr18:12701387..12704274,11	K562	blood:
5	chr18:12378897..12381874-chr18:12386354..12388676,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AFG3L2-2	chr18:12378902-12379263	NONHSAT058367

No data

Variant related genes	Relation type
ENSG00000101624	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000251937	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10853225	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11080564	0.80[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap]
rs11080571	0.85[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs11080572	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1129115	0.85[CEU][hapmap]
rs11553521	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11662523	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11663837	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11664216	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11875938	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12455273	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12456857	0.80[CEU][hapmap]
rs12604732	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12954686	0.83[EUR][1000 genomes]
rs12968089	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12968566	0.85[EUR][1000 genomes]
rs1547858	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1941222	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2003881	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298542	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2298543	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2509510	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28372882	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35968035	0.96[ASN][1000 genomes]
rs3786260	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4797677	0.80[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4797680	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs553091	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs693449	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231182	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7231409	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7235237	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7235296	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7407640	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7504908	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap]
rs7504974	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs7505834	0.80[CEU][hapmap]
rs8086993	0.80[CHD][hapmap];0.87[GIH][hapmap]
rs8092506	0.80[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap]
rs8093375	0.95[CEU][hapmap]
rs8097342	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9303769	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9303770	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap]
rs9303771	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9635829	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9956171	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9960103	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9964406	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1060728	chr18:12364077-12410409	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs478088	TUBB6	cis	lymphoblastoid	seeQTL
rs478088	MEST	trans	lymphoblastoid	seeQTL
rs478088	TUBB6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12378200-12386600	Weak transcription	Fetal Brain Male	brain
2	chr18:12378400-12382000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr18:12378600-12379200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links