Variant report

Variant	rs10031539
Chromosome Location	chr4:21759229-21759230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10002460	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10006785	0.97[ASN][1000 genomes]
rs10012055	0.80[GIH][hapmap]
rs10012747	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs10016234	0.97[ASN][1000 genomes]
rs10028323	0.86[EUR][1000 genomes]
rs10034603	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10938858	0.88[CHB][hapmap]
rs12498561	0.88[CHB][hapmap]
rs12503736	0.88[CHB][hapmap]
rs12642578	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646630	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1349384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1380270	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1459271	0.80[GIH][hapmap]
rs1459274	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1471221	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1562815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs168625	0.88[CHB][hapmap]
rs17498679	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17498715	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1809267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1827590	0.83[EUR][1000 genomes]
rs1827591	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap]
rs1841182	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1841185	0.83[CHB][hapmap]
rs1841186	0.83[CHB][hapmap]
rs1968778	0.88[CHB][hapmap]
rs1985182	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1993037	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2007970	0.82[CHB][hapmap]
rs2007971	0.87[CHB][hapmap]
rs2018175	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28667579	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34833395	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs35609084	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4282162	0.88[CHB][hapmap]
rs4377576	0.88[CHB][hapmap]
rs4563486	0.88[CHB][hapmap]
rs6448069	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6448070	0.83[EUR][1000 genomes]
rs6448072	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs6448073	0.86[EUR][1000 genomes]
rs6448075	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs6840539	0.82[CHB][hapmap]
rs6856781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7375384	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7378252	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs7664617	0.83[CHB][hapmap]
rs896121	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9291430	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs966045	0.83[CHB][hapmap]
rs9884923	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs9994945	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817467	chr4:21602921-22422816	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv878751	chr4:21712050-21793807	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10031539	ZCCHC4	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21752200-21764600	Weak transcription	HMEC	breast
2	chr4:21755400-21764000	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links