Variant report

Variant	rs968008
Chromosome Location	chr5:127825485-127825486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10040416	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10041869	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs10055617	0.87[ASW][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap]
rs10063393	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs10070076	0.82[AFR][1000 genomes]
rs10074194	0.82[AFR][1000 genomes]
rs10074198	0.82[AFR][1000 genomes]
rs10519994	0.87[ASW][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.84[AFR][1000 genomes]
rs10520003	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11949017	1.00[ASW][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11950890	0.82[AFR][1000 genomes]
rs11951267	0.80[EUR][1000 genomes]
rs11955447	0.82[AFR][1000 genomes]
rs11955937	0.80[EUR][1000 genomes]
rs13360784	0.82[AFR][1000 genomes]
rs1396477	0.87[ASW][hapmap];0.83[GIH][hapmap]
rs1435512	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1561006	0.83[GIH][hapmap]
rs17164083	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17164086	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17615636	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17677244	0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs1848501	0.82[AFR][1000 genomes]
rs3792873	0.81[EUR][1000 genomes]
rs4380709	0.80[EUR][1000 genomes]
rs4400171	0.80[EUR][1000 genomes]
rs4425555	0.80[EUR][1000 genomes]
rs4425556	0.80[EUR][1000 genomes]
rs4496752	0.80[EUR][1000 genomes]
rs4577751	0.80[EUR][1000 genomes]
rs4580821	0.80[EUR][1000 genomes]
rs4620068	0.80[EUR][1000 genomes]
rs4836374	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55657505	0.90[EUR][1000 genomes]
rs55683423	0.80[EUR][1000 genomes]
rs55715053	0.90[EUR][1000 genomes]
rs55839668	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55944506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56072924	0.90[EUR][1000 genomes]
rs56173634	0.80[EUR][1000 genomes]
rs56232757	0.80[EUR][1000 genomes]
rs56766733	0.80[EUR][1000 genomes]
rs57454105	0.80[EUR][1000 genomes]
rs58143160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58295967	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59143127	0.80[EUR][1000 genomes]
rs59820839	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs60324229	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60574263	0.80[EUR][1000 genomes]
rs61375240	0.80[EUR][1000 genomes]
rs6595840	0.80[EUR][1000 genomes]
rs6863062	0.80[EUR][1000 genomes]
rs6863262	0.80[EUR][1000 genomes]
rs6863380	0.80[EUR][1000 genomes]
rs6863460	0.80[EUR][1000 genomes]
rs6865828	0.91[EUR][1000 genomes]
rs6873360	1.00[CEU][hapmap]
rs6876609	0.80[EUR][1000 genomes]
rs6880762	0.80[EUR][1000 genomes]
rs6883276	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs6891153	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6891166	0.80[EUR][1000 genomes]
rs73346354	0.91[EUR][1000 genomes]
rs73348070	0.80[EUR][1000 genomes]
rs73348077	0.80[EUR][1000 genomes]
rs73348080	0.80[EUR][1000 genomes]
rs73348085	0.80[EUR][1000 genomes]
rs73348087	0.80[EUR][1000 genomes]
rs73348099	0.80[EUR][1000 genomes]
rs73348102	0.80[EUR][1000 genomes]
rs73348278	0.91[EUR][1000 genomes]
rs73348280	0.91[EUR][1000 genomes]
rs73348283	0.88[EUR][1000 genomes]
rs73348287	0.91[EUR][1000 genomes]
rs73348295	0.90[EUR][1000 genomes]
rs73348299	0.80[EUR][1000 genomes]
rs73350104	0.80[EUR][1000 genomes]
rs73350106	0.80[EUR][1000 genomes]
rs73350109	0.80[EUR][1000 genomes]
rs73350115	0.80[EUR][1000 genomes]
rs73350129	0.80[EUR][1000 genomes]
rs73350195	0.80[EUR][1000 genomes]
rs73352205	0.80[EUR][1000 genomes]
rs73352207	0.80[EUR][1000 genomes]
rs73352225	0.80[EUR][1000 genomes]
rs7447218	0.80[EUR][1000 genomes]
rs764369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7700287	0.80[EUR][1000 genomes]
rs7704921	0.80[EUR][1000 genomes]
rs7709202	0.80[EUR][1000 genomes]
rs7709582	1.00[ASN][1000 genomes]
rs7709634	0.80[EUR][1000 genomes]
rs7714023	0.80[EUR][1000 genomes]
rs7714465	0.80[EUR][1000 genomes]
rs7720190	0.80[EUR][1000 genomes]
rs7728409	0.80[EUR][1000 genomes]
rs7730875	0.80[EUR][1000 genomes]
rs7731176	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7732171	0.80[EUR][1000 genomes]
rs7734405	0.80[EUR][1000 genomes]
rs7734534	0.80[EUR][1000 genomes]
rs892864	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs989548	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs989549	0.87[ASW][hapmap];0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv599698	chr5:127744825-127850855	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	nsv1015650	chr5:127745955-127866566	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1019560	chr5:127814656-127873680	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv537895	chr5:127814656-127873680	ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs968008	FBN2	cis	multi-tissue	Pritchard
rs968008	FBN2	cis	Whole Blood	GTEx
rs968008	FBN2	cis	Artery Tibial	GTEx
rs968008	FBN2	cis	Artery Aorta	GTEx
rs968008	FBN2	cis	Nerve Tibial	GTEx
rs968008	FBN2	cis	Adipose Subcutaneous	GTEx
rs968008	FBN2	cis	lung	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127773400-127830000	Weak transcription	NHEK	skin
2	chr5:127784000-127826800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:127796400-127826600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:127800400-127845600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:127800800-127827000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:127803400-127839200	Weak transcription	Fetal Stomach	stomach
7	chr5:127806400-127830400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:127806400-127847000	Weak transcription	NHDF-Ad	bronchial
9	chr5:127806600-127827000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:127806600-127839600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:127806600-127839600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:127806600-127839600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:127810800-127839400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr5:127811000-127835200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:127816400-127836600	Weak transcription	Placenta	Placenta
16	chr5:127819000-127827000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:127820800-127827000	Weak transcription	Fetal Heart	heart
18	chr5:127823000-127826600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:127823000-127839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:127824000-127835800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:127824800-127853800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:127825000-127827400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:127825400-127826200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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