Variant report

Variant	rs10980396
Chromosome Location	chr9:99826216-99826217
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	chr9:99801323..99803187-chr9:99824976..99826647,2	MCF-7	breast:
2	chr9:99799772..99802135-chr9:99823407..99826313,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136943	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10114720	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10115220	0.86[EUR][1000 genomes]
rs10118886	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10118923	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10123754	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10123757	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10739289	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10739296	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759391	0.81[EUR][1000 genomes]
rs10759399	0.82[ASN][1000 genomes]
rs10759400	0.87[ASN][1000 genomes]
rs10759406	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10759417	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759420	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816926	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10816951	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10816953	0.83[ASN][1000 genomes]
rs10816962	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10816963	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10816964	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10816981	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816984	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816994	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817013	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10980326	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10980346	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12236690	0.85[ASN][1000 genomes]
rs12376012	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12376575	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12377546	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13285842	0.93[ASN][1000 genomes]
rs15394	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16924211	0.94[ASN][1000 genomes]
rs2004336	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34342973	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4367680	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501700	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4510972	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59995818	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62560873	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6477844	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7023974	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7035822	0.81[EUR][1000 genomes]
rs7038926	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7039198	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7857836	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7873286	0.85[ASN][1000 genomes]
rs7875800	0.81[EUR][1000 genomes]
rs9792463	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428540	chr9:99722815-99863455	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99816200-99834600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:99825200-99826400	Weak transcription	Stomach Mucosa	stomach
3	chr9:99825400-99826400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:99825400-99826600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:99825600-99829800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:99825800-99826600	Weak transcription	HMEC	breast
7	chr9:99826000-99827000	Enhancers	Fetal Intestine Large	intestine
8	chr9:99826000-99827000	Enhancers	Fetal Intestine Small	intestine
9	chr9:99826200-99826400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:99826200-99826800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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