Variant report

Variant	rs4400171
Chromosome Location	chr5:127882627-127882628
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127881388..127883013-chr5:127901894..127903649,2	MCF-7	breast:

Extended variants
information (count: 140 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10520003	0.80[EUR][1000 genomes]
rs11241965	0.80[AFR][1000 genomes]
rs11949649	0.80[AFR][1000 genomes]
rs11949660	0.82[AFR][1000 genomes]
rs11949692	0.80[AFR][1000 genomes]
rs11951267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11952524	0.87[AFR][1000 genomes]
rs11953201	0.80[AFR][1000 genomes]
rs11954906	1.00[ASN][1000 genomes]
rs11955937	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11958508	0.81[AFR][1000 genomes]
rs13153799	0.80[AFR][1000 genomes]
rs13153812	0.80[AFR][1000 genomes]
rs13167932	0.80[AFR][1000 genomes]
rs13173782	0.80[AFR][1000 genomes]
rs1363469	0.88[EUR][1000 genomes]
rs17164083	0.82[EUR][1000 genomes]
rs17164086	0.82[EUR][1000 genomes]
rs34012094	0.81[AFR][1000 genomes]
rs34881645	0.80[AFR][1000 genomes]
rs35043622	0.80[AFR][1000 genomes]
rs36125852	0.80[AFR][1000 genomes]
rs4380709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4386769	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4410683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4425555	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4425556	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4493716	0.91[EUR][1000 genomes]
rs4496752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4557470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4577751	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4580821	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4620068	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55657505	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs55683423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55696017	0.91[EUR][1000 genomes]
rs55715053	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs55791343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55840580	0.91[EUR][1000 genomes]
rs55944506	0.80[EUR][1000 genomes]
rs56018106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56072924	0.87[EUR][1000 genomes]
rs56173634	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56232757	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56358260	0.88[EUR][1000 genomes]
rs56766733	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57454105	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58143160	0.80[EUR][1000 genomes]
rs58295967	0.80[EUR][1000 genomes]
rs58349179	0.91[EUR][1000 genomes]
rs59143127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59567527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60324229	0.80[EUR][1000 genomes]
rs60574263	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61081409	0.91[EUR][1000 genomes]
rs61358597	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61375240	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62390696	0.80[AFR][1000 genomes]
rs62390702	0.80[AFR][1000 genomes]
rs6595840	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6863062	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6863262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6863380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6863460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6865828	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6870737	0.80[AFR][1000 genomes]
rs6870746	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6871698	0.80[AFR][1000 genomes]
rs6876609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6877748	0.80[AFR][1000 genomes]
rs6877872	0.80[AFR][1000 genomes]
rs6877956	0.80[AFR][1000 genomes]
rs6878062	0.80[AFR][1000 genomes]
rs6878172	0.80[AFR][1000 genomes]
rs6880762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6886451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6891153	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6891166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6892406	0.80[AFR][1000 genomes]
rs73334912	0.80[AFR][1000 genomes]
rs73346354	0.88[EUR][1000 genomes]
rs73348066	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73348070	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73348077	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73348078	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73348080	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73348085	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73348087	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73348099	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73348102	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73348278	0.88[EUR][1000 genomes]
rs73348280	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73348283	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73348287	0.88[EUR][1000 genomes]
rs73348295	0.87[EUR][1000 genomes]
rs73348296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73348299	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73350104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73350106	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73350109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73350115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73350129	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73350134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73350195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73351861	0.91[EUR][1000 genomes]
rs73351865	0.91[EUR][1000 genomes]
rs73351884	0.91[EUR][1000 genomes]
rs73352205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73352207	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73352225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73352737	0.86[EUR][1000 genomes]
rs73352741	0.86[EUR][1000 genomes]
rs73352743	0.86[EUR][1000 genomes]
rs7446266	1.00[ASN][1000 genomes]
rs7447218	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs764369	0.80[EUR][1000 genomes]
rs7700287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7704921	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709202	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709476	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7709634	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7714023	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7714465	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7714623	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7720190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7724233	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7724383	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7725452	0.80[AFR][1000 genomes]
rs7727413	0.82[AFR][1000 genomes]
rs7728409	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7730875	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7732171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7734405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7734534	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7735831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs892864	0.80[EUR][1000 genomes]
rs968008	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv530822	chr5:127777365-127900742	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv427734	chr5:127805281-128088632	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4400171	FBN2	cis	lung	GTEx
rs4400171	FBN2	cis	Artery Aorta	GTEx
rs4400171	FBN2	cis	Whole Blood	GTEx
rs4400171	FBN2	cis	Adipose Subcutaneous	GTEx
rs4400171	FBN2	cis	Nerve Tibial	GTEx
rs4400171	FBN2	cis	Artery Tibial	GTEx
rs4400171	FBN2	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127882200-127883200	Enhancers	NHEK	skin
2	chr5:127882200-127883400	Enhancers	Placenta Amnion	Placenta Amnion
3	chr5:127882400-127882800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:127882400-127883000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:127882400-127883000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:127882400-127883200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:127882400-127883200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:127882400-127883600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:127882400-127883600	Enhancers	Placenta	Placenta
10	chr5:127882600-127883200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr5:127882600-127883200	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links