Variant report

Variant	rs1405718
Chromosome Location	chr2:178499809-178499810
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:178497999..178500939-chr2:178626259..178628565,2	K562	blood:
2	chr2:178499231..178501761-chr2:178503904..178506555,2	K562	blood:
3	chr2:178196424..178198872-chr2:178498721..178501636,2	K562	blood:
4	chr2:178494059..178496707-chr2:178497248..178499887,2	K562	blood:
5	chr2:178480859..178483355-chr2:178499342..178501117,2	K562	blood:
6	chr2:178485267..178487759-chr2:178497863..178500182,2	K562	blood:
7	chr2:178482484..178484569-chr2:178497443..178499895,2	K562	blood:
8	chr2:178490562..178493751-chr2:178498705..178503907,5	K562	blood:
9	chr2:178489030..178493776-chr2:178494411..178499893,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197557	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10167783	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1047884	0.94[JPT][hapmap]
rs11678875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11682717	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11682753	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11890088	0.85[ASN][1000 genomes]
rs12467363	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469884	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12471621	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475108	0.89[ASN][1000 genomes]
rs12611503	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12612481	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12616259	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12616288	0.83[AFR][1000 genomes]
rs12990878	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12990917	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12994392	0.86[ASN][1000 genomes]
rs12997716	0.93[ASN][1000 genomes]
rs13008833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13008857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13009207	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13020788	0.84[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs13027895	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13031008	0.80[ASN][1000 genomes]
rs13034781	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1358328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1405714	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1405717	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527401	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1527406	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1527407	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1530034	0.85[JPT][hapmap]
rs1544002	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2222711	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770005	0.82[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770007	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3770008	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3770009	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770010	0.86[ASN][1000 genomes]
rs3770011	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770012	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821006	0.86[ASN][1000 genomes]
rs4144275	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4144276	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4337505	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4893838	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4893969	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs55792594	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433684	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6734528	0.84[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs6736390	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7578325	0.84[ASN][1000 genomes]
rs7605493	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7605609	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605757	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs880897	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs880898	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs880899	0.89[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1405718	TTC30A	cis	Lymphoblastoid	GTEx
rs1405718	TTC30A	cis	lymphoblastoid	seeQTL
rs1405718	TTC30B	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178498600-178500000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:178499000-178500000	Weak transcription	Brain Germinal Matrix	brain
3	chr2:178499200-178500000	Enhancers	Fetal Brain Male	brain
4	chr2:178499200-178500200	Enhancers	Left Ventricle	heart
5	chr2:178499200-178503400	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:178499200-178503600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:178499200-178505400	Weak transcription	Fetal Lung	lung
8	chr2:178499400-178500000	Flanking Active TSS	Dnd41	blood
9	chr2:178499400-178500000	Flanking Active TSS	GM12878-XiMat	blood
10	chr2:178499600-178500000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:178499800-178500000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr2:178499800-178500000	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:178499800-178500000	Enhancers	Fetal Brain Female	brain
14	chr2:178499800-178500000	Enhancers	K562	blood
15	chr2:178499800-178500200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:178499800-178500200	Enhancers	Adipose Nuclei	Adipose
17	chr2:178499800-178504000	Weak transcription	Right Atrium	heart
18	chr2:178499800-178505400	Weak transcription	Fetal Kidney	kidney

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