Variant report

Variant	rs10072459
Chromosome Location	chr5:75462736-75462737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr5:75462668-75462997	GM12878	blood:	n/a	chr5:75462833-75462842 chr5:75462833-75462842
2	CREB1	chr5:75462653-75463210	GM12878	blood:	n/a	n/a
3	NFIC	chr5:75462698-75463031	GM12878	blood:	n/a	n/a
4	RUNX3	chr5:75462428-75463110	GM12878	blood:	n/a	chr5:75462833-75462842 chr5:75462833-75462842
5	CREB1	chr5:75462671-75463124	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000251668	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10066377	0.85[CEU][hapmap]
rs10066725	1.00[CEU][hapmap]
rs11955072	1.00[CEU][hapmap]
rs12188684	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189418	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522618	0.85[CEU][hapmap]
rs12522790	0.90[ASN][1000 genomes]
rs1895390	0.85[CEU][hapmap]
rs2059156	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28581866	0.84[ASN][1000 genomes]
rs3922565	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4274961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299714	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4309948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364364	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4371731	1.00[ASN][1000 genomes]
rs4610441	0.85[CEU][hapmap]
rs6879305	1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6879785	0.84[CHD][hapmap];0.83[MEX][hapmap]
rs6889023	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6897128	1.00[CEU][hapmap]
rs6897302	1.00[CEU][hapmap]
rs6898301	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6898618	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71585074	0.85[EUR][1000 genomes]
rs7726643	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1034853	chr5:75382047-75534981	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv462212	chr5:75388834-75534570	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv598676	chr5:75388834-75534570	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv526084	chr5:75410511-75530494	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv2757119	chr5:75426863-75474780	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv2759351	chr5:75426863-75474780	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv34958	chr5:75429015-75474921	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10072459	FCHO2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75461200-75465200	Weak transcription	Brain Anterior Caudate	brain

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