Variant report

Variant	rs10992489
Chromosome Location	chr9:95605067-95605068
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	chr9:95598967..95600808-chr9:95603300..95605228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226721	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10115872	0.87[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10123843	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10123870	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10156497	0.98[ASN][1000 genomes]
rs1022833	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739932	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739933	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739934	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739938	0.82[AMR][1000 genomes]
rs10761172	0.98[ASN][1000 genomes]
rs10761175	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821021	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10821022	0.98[ASN][1000 genomes]
rs10821028	0.98[ASN][1000 genomes]
rs10821030	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821031	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821032	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10821035	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821040	0.81[ASN][1000 genomes]
rs10992529	0.81[ASN][1000 genomes]
rs12003440	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs12336022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12337654	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12338961	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12346689	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12379300	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13288901	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13293147	0.86[JPT][hapmap]
rs13294147	0.84[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2296060	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs28700150	0.95[ASN][1000 genomes]
rs36194652	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3824428	0.98[ASN][1000 genomes]
rs4078292	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4133033	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4535796	0.84[ASN][1000 genomes]
rs4538949	0.81[ASN][1000 genomes]
rs4626670	0.81[ASN][1000 genomes]
rs4744150	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744151	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479434	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7032277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7035881	0.86[JPT][hapmap]
rs7039812	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7040645	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7043469	0.86[JPT][hapmap]
rs7045305	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7847713	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7847998	0.98[ASN][1000 genomes]
rs7859380	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs7869480	0.98[ASN][1000 genomes]
rs7872848	0.81[ASN][1000 genomes]
rs7872987	0.81[ASN][1000 genomes]
rs7873021	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7874026	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9775485	0.81[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	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv893574	chr9:95580376-95688099	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv525363	chr9:95598200-95605067	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10992489	ZNF484	cis	parietal	SCAN
rs10992489	ZNF484	cis	cerebellum	SCAN
rs10992489	C9orf102	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95598000-95616800	ZNF genes & repeats	Liver	Liver
2	chr9:95599800-95608400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:95600000-95608400	Weak transcription	Placenta	Placenta
4	chr9:95600000-95610000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:95601000-95605800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:95603000-95607800	Weak transcription	NH-A	brain
7	chr9:95603200-95608000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:95603400-95616200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:95603600-95609000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:95604400-95608400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:95604600-95607600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:95605000-95605400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:95605000-95605600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
14	chr9:95605000-95605600	ZNF genes & repeats	A549	lung
15	chr9:95605000-95608400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:95605000-95611200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:95605000-95624200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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