Variant report

Variant	rs4538949
Chromosome Location	chr9:95681227-95681228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95680955..95683491-chr9:95687222..95689030,2	K562	blood:
2	chr9:95677020..95680081-chr9:95681150..95683718,3	MCF-7	breast:
3	chr9:95680681..95683680-chr9:95689468..95691855,3	MCF-7	breast:

Extended variants
information (count: 60 )
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];0.86[CHD][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10123843	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10123870	0.86[EUR][1000 genomes]
rs10156497	0.82[ASN][1000 genomes]
rs1022833	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10739932	0.83[ASN][1000 genomes]
rs10739933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739934	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10761172	0.82[ASN][1000 genomes]
rs10821021	0.82[ASN][1000 genomes]
rs10821022	0.82[ASN][1000 genomes]
rs10821028	0.82[ASN][1000 genomes]
rs10821030	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821031	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821032	0.83[ASN][1000 genomes]
rs10821035	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821040	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992489	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs10992529	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003440	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs12336022	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12337654	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12338961	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12346689	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12379300	0.82[ASN][1000 genomes]
rs13288901	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13293147	0.86[JPT][hapmap]
rs13294147	0.84[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2296060	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35449185	0.83[ASN][1000 genomes]
rs36194652	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3824428	0.82[ASN][1000 genomes]
rs4078292	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs4133033	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4510923	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4535796	0.97[ASN][1000 genomes]
rs4626670	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744150	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744151	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6479434	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7024752	0.83[ASN][1000 genomes]
rs7032277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7035868	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7035881	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs7039812	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7040645	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7043469	0.86[JPT][hapmap]
rs7045305	0.82[ASN][1000 genomes]
rs7047181	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7847713	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7847998	0.82[ASN][1000 genomes]
rs7869480	0.82[ASN][1000 genomes]
rs7872848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872987	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873021	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7874026	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1818795	chr9:95656340-95689158	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	nsv982639	chr9:95671744-95685131	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4538949	ZNF484	cis	parietal	SCAN
rs4538949	ZNF484	cis	cerebellum	SCAN
rs4538949	C9orf102	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95674800-95687400	Weak transcription	Right Atrium	heart
2	chr9:95675800-95683400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:95680000-95682800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:95680200-95681600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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