Variant report

Variant	rs7869985
Chromosome Location	chr9:103129992-103129993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103113675..103115491-chr9:103128781..103131501,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136891	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10117799	0.88[ASN][1000 genomes]
rs10118398	0.98[ASN][1000 genomes]
rs10118701	0.88[ASN][1000 genomes]
rs10120244	0.97[ASN][1000 genomes]
rs10123866	0.88[ASN][1000 genomes]
rs10123913	0.88[ASN][1000 genomes]
rs10124133	0.98[ASN][1000 genomes]
rs10124893	0.87[ASN][1000 genomes]
rs10125785	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10760724	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10819751	0.86[ASN][1000 genomes]
rs10819756	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10819759	0.92[ASN][1000 genomes]
rs10819761	0.95[ASN][1000 genomes]
rs10819762	0.98[ASN][1000 genomes]
rs10819764	0.98[ASN][1000 genomes]
rs10819767	0.98[ASN][1000 genomes]
rs10989049	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10989056	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10989064	0.98[ASN][1000 genomes]
rs10989067	0.98[ASN][1000 genomes]
rs10989070	0.98[ASN][1000 genomes]
rs11789196	0.88[ASN][1000 genomes]
rs12684939	0.92[ASN][1000 genomes]
rs1338123	0.86[ASN][1000 genomes]
rs1338124	0.86[ASN][1000 genomes]
rs1338125	0.86[ASN][1000 genomes]
rs1930243	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1930244	0.91[ASN][1000 genomes]
rs1961367	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026999	0.98[ASN][1000 genomes]
rs2151131	0.91[ASN][1000 genomes]
rs2210498	0.98[ASN][1000 genomes]
rs2245216	0.85[ASN][1000 genomes]
rs2417084	0.98[ASN][1000 genomes]
rs2417176	0.98[ASN][1000 genomes]
rs2485745	0.83[ASN][1000 genomes]
rs2787368	0.88[ASN][1000 genomes]
rs2787369	0.88[ASN][1000 genomes]
rs2787371	0.87[ASN][1000 genomes]
rs2787372	0.88[ASN][1000 genomes]
rs2787373	0.88[ASN][1000 genomes]
rs2787375	0.88[ASN][1000 genomes]
rs2787376	0.81[ASN][1000 genomes]
rs2787377	0.90[ASN][1000 genomes]
rs2787380	0.85[ASN][1000 genomes]
rs2787381	0.85[ASN][1000 genomes]
rs2787383	0.86[ASN][1000 genomes]
rs2787385	0.85[ASN][1000 genomes]
rs2787388	0.86[ASN][1000 genomes]
rs2806692	0.86[ASN][1000 genomes]
rs2806693	0.83[ASN][1000 genomes]
rs2806694	0.83[ASN][1000 genomes]
rs2806695	0.85[ASN][1000 genomes]
rs2806696	0.86[ASN][1000 genomes]
rs2806702	0.90[ASN][1000 genomes]
rs2806703	0.87[ASN][1000 genomes]
rs28464821	0.95[ASN][1000 genomes]
rs3813712	0.90[ASN][1000 genomes]
rs3923501	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4128230	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4237194	0.92[EUR][1000 genomes]
rs4237195	0.88[ASN][1000 genomes]
rs4237196	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4446782	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742782	0.88[ASN][1000 genomes]
rs4742783	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742784	0.95[ASN][1000 genomes]
rs4743392	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743393	0.92[ASN][1000 genomes]
rs4743394	0.95[ASN][1000 genomes]
rs4743395	0.98[ASN][1000 genomes]
rs4743396	0.98[ASN][1000 genomes]
rs5029342	0.88[ASN][1000 genomes]
rs5029343	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59242794	0.95[ASN][1000 genomes]
rs6479008	0.85[ASN][1000 genomes]
rs6479009	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6479010	0.89[EUR][1000 genomes]
rs6479011	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6479013	0.85[ASN][1000 genomes]
rs6479014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020988	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7021310	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025891	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7025938	0.88[ASN][1000 genomes]
rs7035619	0.88[ASN][1000 genomes]
rs7036570	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047694	0.92[ASN][1000 genomes]
rs7048601	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7472	0.88[ASN][1000 genomes]
rs7849966	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7852189	0.98[ASN][1000 genomes]
rs7854693	0.88[ASN][1000 genomes]
rs7860513	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864494	0.88[ASN][1000 genomes]
rs7866850	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871702	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874900	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875775	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914711	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299338	0.98[ASN][1000 genomes]
rs944710	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946054	0.85[ASN][1000 genomes]
rs959893	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9775014	0.84[ASN][1000 genomes]
rs9775182	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7869985	INVS	cis	multi-tissue	Pritchard
rs7869985	INVS	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103116600-103131000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr9:103125200-103135400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:103129600-103131800	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr9:103129800-103131800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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