Variant report

Variant	rs4896488
Chromosome Location	chr6:140123580-140123581
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	chr6:140123522..140126295-chr6:140134268..140137009,2	K562	blood:
2	chr6:140101468..140104254-chr6:140123458..140124998,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11964275	1.00[CEU][hapmap]
rs11965819	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069373	0.88[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1936214	0.82[AMR][1000 genomes]
rs2154032	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs4568471	0.92[ASN][1000 genomes]
rs60052799	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570374	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs6901783	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6904036	0.92[ASN][1000 genomes]
rs6905478	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs6911905	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926194	0.93[ASN][1000 genomes]
rs6933318	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6933569	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73775693	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772473	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772713	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7774968	1.00[CEU][hapmap]
rs7776193	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376463	0.88[ASN][1000 genomes]
rs9376464	0.97[ASN][1000 genomes]
rs9376466	0.93[ASN][1000 genomes]
rs9385874	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs9385879	0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs9389723	0.93[ASN][1000 genomes]
rs9399293	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403115	1.00[CEU][hapmap]
rs9403124	0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9403125	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1022881	chr6:140098646-140172570	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	nsv886692	chr6:140111650-140155090	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4896488	MAP3K5	cis	parietal	SCAN
rs4896488	NHSL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140123400-140125400	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links