Variant report

Variant	rs10946694
Chromosome Location	chr6:24376579-24376580
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	chr6:24355293..24358051-chr6:24374939..24377466,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146049	Chromatin interaction
ENSG00000146038	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12196464	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525718	0.86[ASN][1000 genomes]
rs12527102	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1629620	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2025033	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2328820	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28824273	0.90[ASN][1000 genomes]
rs4382236	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6456608	0.83[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6904234	0.86[JPT][hapmap]
rs6913986	0.90[ASN][1000 genomes]
rs6940827	0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs714452	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7751169	0.80[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs7758878	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7768604	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7775357	0.81[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs793649	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs793650	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793658	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs793659	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793662	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793663	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793666	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793676	0.82[CEU][hapmap]
rs793694	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793698	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793699	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793701	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793703	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793720	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs793721	0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs793722	0.83[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs811102	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs811103	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs811578	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9295623	0.82[ASN][1000 genomes]
rs9366569	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467121	0.83[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs9467123	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467124	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467126	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467134	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467135	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10946694	ZKSCAN4	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24372800-24381600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:24375600-24376600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:24375600-24376600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:24376200-24376600	Strong transcription	HepG2	liver
5	chr6:24376200-24376800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:24376400-24376800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:24376400-24376800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:24376400-24377400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:24376400-24377600	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links