Variant report

Variant	rs4090603
Chromosome Location	chr5:59779073-59779074
allele	A/T
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	FOS	chr5:59779008-59779089	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr5:59779000-59779142	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr5:59778990-59779125	MCF10A-Er-Src	breast:	n/a	n/a
4	FOSL2	chr5:59778773-59779281	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr5:59778948-59779173	A549	lung:	n/a	n/a

Variant related genes	Relation type
PART1	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10514893	1.00[CEU][hapmap]
rs10514894	1.00[CEU][hapmap]
rs10939848	0.97[ASN][1000 genomes]
rs1423471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[ASN][1000 genomes]
rs152327	0.80[YRI][hapmap]
rs16877896	1.00[CEU][hapmap]
rs16877898	1.00[CEU][hapmap]
rs16877901	1.00[CEU][hapmap]
rs16877933	1.00[CEU][hapmap]
rs16877936	1.00[CEU][hapmap]
rs16877964	1.00[CEU][hapmap]
rs16877967	1.00[CEU][hapmap]
rs16877993	0.91[CHB][hapmap]
rs16878035	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs16878037	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs16878086	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs16878104	1.00[CEU][hapmap];0.98[ASN][1000 genomes]
rs16878106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16878108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17326404	1.00[CEU][hapmap]
rs17378750	1.00[CEU][hapmap]
rs1862589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2409102	0.97[ASN][1000 genomes]
rs3763059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4130444	1.00[CEU][hapmap]
rs4580738	1.00[CEU][hapmap]
rs55737169	0.97[ASN][1000 genomes]
rs56151644	0.84[EUR][1000 genomes]
rs56217581	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58376959	0.84[EUR][1000 genomes]
rs58891299	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59313902	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60104228	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60257457	0.97[ASN][1000 genomes]
rs61166140	0.93[ASN][1000 genomes]
rs61379877	0.97[ASN][1000 genomes]
rs6449471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6864442	0.91[CHB][hapmap]
rs6878429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6887545	0.90[CHB][hapmap]
rs6887925	0.91[CHB][hapmap]
rs6891858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs73108666	0.96[ASN][1000 genomes]
rs73108670	0.97[ASN][1000 genomes]
rs73108674	0.97[ASN][1000 genomes]
rs73759052	0.84[EUR][1000 genomes]
rs73759053	0.84[EUR][1000 genomes]
rs7702188	1.00[CEU][hapmap]
rs7702474	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.98[ASN][1000 genomes]
rs7705194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[ASN][1000 genomes]
rs7712662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs7723861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7725629	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[EUR][1000 genomes]
rs7734108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[ASN][1000 genomes]
rs7737086	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59741800-59783200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:59767200-59789000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:59777600-59781400	Weak transcription	Aorta	Aorta
4	chr5:59778000-59779200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:59778200-59779200	Enhancers	HMEC	breast
6	chr5:59778200-59779200	Enhancers	NHEK	skin
7	chr5:59778200-59779800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr5:59778400-59779400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:59778400-59779400	Weak transcription	HSMM	muscle
10	chr5:59778400-59779800	Weak transcription	HepG2	liver
11	chr5:59778800-59779200	Weak transcription	A549	lung
12	chr5:59779000-59780000	Weak transcription	Placenta Amnion	Placenta Amnion

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