Variant report

Variant	rs2025033
Chromosome Location	chr6:24385346-24385347
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24384186..24386194-chr6:24388139..24390606,2	MCF-7	breast:
2	chr6:24382936..24386801-chr6:24387584..24390590,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10946694	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12192494	0.86[JPT][hapmap]
rs12192603	0.86[JPT][hapmap]
rs12196464	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12527102	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1629620	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2328820	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28824273	0.83[ASN][1000 genomes]
rs4382236	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4599626	0.86[JPT][hapmap]
rs6456608	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913986	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940827	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs714452	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7751169	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7758878	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7768604	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7770684	0.85[JPT][hapmap]
rs7775357	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793649	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793650	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793651	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs793658	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs793659	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793660	0.88[EUR][1000 genomes]
rs793662	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793663	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793666	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793676	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs793694	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793698	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793699	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793701	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793703	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793720	0.85[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793721	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793722	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs811102	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs811103	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811578	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366569	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467121	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[ASN][1000 genomes]
rs9467123	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467124	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467126	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467129	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467134	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467135	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2025033	ZKSCAN4	cis	cerebellum	SCAN
rs2025033	HIST1H2AC	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24384200-24385800	Weak transcription	A549	lung
2	chr6:24384400-24385400	Weak transcription	Fetal Intestine Large	intestine
3	chr6:24385200-24385600	Flanking Active TSS	HepG2	liver
4	chr6:24385200-24386600	Enhancers	Fetal Intestine Small	intestine
5	chr6:24385200-24386800	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links