Variant report

Variant	rs11242579
Chromosome Location	chr5:98395559-98395560
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	chr5:98263463..98264993-chr5:98394604..98397406,2	K562	blood:
2	chr5:98367873..98368452-chr5:98395154..98396281,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10040066	0.90[JPT][hapmap]
rs10054188	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10056306	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10060754	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10064016	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11742975	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750764	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12659212	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12659251	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1472622	0.88[JPT][hapmap]
rs2121666	0.80[ASN][1000 genomes]
rs2121668	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2369574	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs366353	0.90[JPT][hapmap]
rs377731	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4128275	0.83[ASN][1000 genomes]
rs4329038	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs539024	0.90[JPT][hapmap]
rs55946434	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56161473	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57544561	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59910509	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61110940	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61198176	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6596673	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6596679	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6596680	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6596681	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6866426	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6888668	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6890939	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7700837	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7712453	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7714788	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7717324	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730642	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7735294	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7735379	0.85[ASN][1000 genomes]
rs7737983	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs819230	0.90[JPT][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	nsv1024391	chr5:98355665-98653657	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv599118	chr5:98358191-99029453	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv599119	chr5:98358191-99315677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98381600-98395800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr5:98387800-98396600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:98388600-98395800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:98391600-98396000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr5:98391800-98395800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr5:98392200-98395800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:98392400-98396600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:98393200-98397800	Enhancers	Primary B cells from peripheral blood	blood
9	chr5:98393600-98396000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:98393800-98396400	Weak transcription	HMEC	breast
11	chr5:98393800-98396600	Weak transcription	HepG2	liver
12	chr5:98394600-98395800	Enhancers	Primary B cells from cord blood	blood
13	chr5:98394600-98396400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:98395000-98398200	Enhancers	GM12878-XiMat	blood
15	chr5:98395200-98396000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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