Variant report

Variant	rs7039118
Chromosome Location	chr9:101566770-101566771
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr9:101566278-101566937	MCF10A-Er-Src	breast:	n/a	n/a
2	NFIC	chr9:101566294-101566859	ECC-1	luminal epithelium:	n/a	n/a
3	MYC	chr9:101566560-101566807	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:101556573..101560424-chr9:101566029..101574080,12	MCF-7	breast:
2	chr9:101550194..101555244-chr9:101566657..101571786,8	MCF-7	breast:
3	chr9:101557242..101560519-chr9:101566443..101572716,8	MCF-7	breast:
4	chr9:100746056..100747789-chr9:101565499..101567347,2	MCF-7	breast:

Variant related genes	Relation type
GALNT12	TF binding region
ENSG00000165138	Chromatin interaction
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10119228	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10125255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739704	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10987230	1.00[CEU][hapmap]
rs10987234	1.00[CEU][hapmap]
rs10987293	1.00[CEU][hapmap]
rs10987843	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1167771	1.00[CEU][hapmap]
rs1555520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs180038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs180039	0.90[ASN][1000 genomes]
rs182877	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1930130	1.00[CEU][hapmap]
rs2058881	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295922	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2778916	1.00[CEU][hapmap]
rs2778919	1.00[CEU][hapmap]
rs2779539	1.00[CEU][hapmap]
rs337527	1.00[CEU][hapmap]
rs337564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337566	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337567	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337568	0.89[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337571	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs337583	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337589	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs337590	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs371521	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4133240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4133831	0.87[EUR][1000 genomes]
rs429562	0.87[EUR][1000 genomes]
rs439347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs453409	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742740	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742742	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743279	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4743280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743283	0.82[EUR][1000 genomes]
rs48418	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs507318	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6415847	0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6415849	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs692824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7029599	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7846846	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7861840	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7867234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867317	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9409306	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs967932	1.00[CEU][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	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101559600-101567600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr9:101559600-101567800	Weak transcription	Stomach Mucosa	stomach
3	chr9:101559600-101569000	Weak transcription	Pancreas	Pancrea
4	chr9:101559600-101569600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:101562600-101569400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:101564400-101567600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr9:101564600-101567600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:101564600-101567800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:101564800-101567400	Weak transcription	HMEC	breast
10	chr9:101564800-101567600	Weak transcription	NHEK	skin
11	chr9:101565400-101567800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:101565400-101569000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:101565800-101567400	Enhancers	Fetal Lung	lung
14	chr9:101565800-101567600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr9:101566000-101567400	Weak transcription	K562	blood
16	chr9:101566000-101567600	Weak transcription	Esophagus	oesophagus
17	chr9:101566200-101569200	Weak transcription	Fetal Stomach	stomach
18	chr9:101566400-101567800	Enhancers	Colon Smooth Muscle	Colon
19	chr9:101566600-101566800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr9:101566600-101567600	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links