Variant report

Variant	rs17079512
Chromosome Location	chr3:47264613-47264614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47256438..47258456-chr3:47263578..47265840,2	K562	blood:
2	chr3:47256140..47258456-chr3:47263578..47266012,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-4	chr3:47263633-47264866	NONHSAT089485

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11712779	0.84[ASN][1000 genomes]
rs12486248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12487863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs12490244	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490251	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490467	1.00[AFR][1000 genomes]
rs12492463	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12493723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs12495173	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495438	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12636235	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17079543	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17079580	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs3733093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3821879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3933020	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4082156	0.92[ASN][1000 genomes]
rs4627772	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683318	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs4683323	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683328	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs58206566	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59601660	0.92[ASN][1000 genomes]
rs7638049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	esv1799921	chr3:47259253-47283105	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	6 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	chr3:47208200-47276600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:47223800-47269200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:47245400-47266600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:47247000-47269400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:47262800-47266200	Weak transcription	Primary B cells from cord blood	blood
6	chr3:47262800-47287400	Weak transcription	Primary T cells from cord blood	blood
7	chr3:47263000-47275600	Weak transcription	HSMMtube	muscle
8	chr3:47263400-47268000	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:47263600-47276600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:47264200-47322200	Weak transcription	Gastric	stomach

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