Variant report

Variant	rs1006042
Chromosome Location	chr4:78133566-78133567
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	chr4:78130169..78132632-chr4:78133437..78136630,3	K562	blood:
2	chr4:78132153..78134677-chr4:78134780..78136645,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10009384	0.87[JPT][hapmap]
rs10010290	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs10018359	0.86[JPT][hapmap]
rs10025838	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10026129	0.87[JPT][hapmap]
rs10030727	0.97[ASN][1000 genomes]
rs10030735	0.87[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10030867	0.81[JPT][hapmap]
rs10030957	0.87[JPT][hapmap]
rs10856957	0.91[JPT][hapmap]
rs11097730	0.87[JPT][hapmap]
rs12504752	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs12508219	0.81[JPT][hapmap]
rs12509168	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12640093	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477314	0.91[JPT][hapmap]
rs1559119	0.91[JPT][hapmap]
rs1559122	0.89[JPT][hapmap]
rs2042228	0.91[JPT][hapmap]
rs4241604	0.84[GIH][hapmap]
rs4280759	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382065	0.83[EUR][1000 genomes]
rs4518274	0.84[GIH][hapmap]
rs4547817	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4563522	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4576030	0.87[JPT][hapmap]
rs4582179	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4582180	0.85[JPT][hapmap]
rs4859475	0.85[JPT][hapmap]
rs4859477	0.90[JPT][hapmap]
rs4859753	0.87[JPT][hapmap]
rs4859754	0.86[JPT][hapmap]
rs4859755	0.87[JPT][hapmap]
rs4859756	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6822794	0.91[JPT][hapmap]
rs6840915	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6845599	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6845942	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846698	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6857792	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7690427	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000730	chr4:78109138-78210296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1011551	chr4:78120872-78204224	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1012298	chr4:78120872-78255427	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv997743	chr4:78126462-78217004	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1014055	chr4:78132200-78255427	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1013602	chr4:78133566-78217004	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1007726	chr4:78133566-78255427	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1006042	CCNG2	cis	cerebellum	SCAN
rs1006042	BMP3	cis	parietal	SCAN
rs1006042	ANTXR2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78125200-78143600	Weak transcription	Primary B cells from cord blood	blood

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