Variant report

Variant	rs1989766
Chromosome Location	chr9:118172285-118172286
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:118172097..118173608-chr9:118174134..118175717,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10124142	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10124377	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10739439	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739440	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10739441	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10739443	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10759774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759775	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10759776	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10759777	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10759778	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10759779	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10817755	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs10817763	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10817765	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10817768	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10817769	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10817772	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10982733	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10982735	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10982738	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10982741	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1156578	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12552121	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12686630	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1335141	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1632812	0.83[EUR][1000 genomes]
rs1632833	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1632836	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1632839	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1632840	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1632845	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2020265	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2020279	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2078713	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2269700	0.83[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2418337	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2418341	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3983324	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3983325	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4978636	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4979525	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6478160	0.83[ASW][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs7022390	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7850103	0.82[ASW][hapmap];0.86[CHB][hapmap];0.80[YRI][hapmap]
rs7872215	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7872813	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs916553	0.83[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409143	0.80[YRI][hapmap]
rs9409144	0.80[YRI][hapmap]
rs9409145	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs9409146	0.80[JPT][hapmap];1.00[YRI][hapmap]

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	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1042957	chr9:118153824-118313540	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1989766	DNAJC25	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118160400-118173600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr9:118162200-118174000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:118170800-118173400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:118170800-118173600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:118171000-118173600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:118171200-118172800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:118171200-118174000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:118171400-118173200	Weak transcription	NHDF-Ad	bronchial
9	chr9:118171400-118173400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:118171600-118172800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:118171800-118174000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr9:118172000-118174000	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links