Variant report

Variant	rs17839642
Chromosome Location	chr5:127833080-127833081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10042096	0.94[ASN][1000 genomes]
rs10053025	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs10477685	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs10478812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10478813	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs10478814	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs11960575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17164094	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs17164113	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs17164127	1.00[CHD][hapmap]
rs1897998	0.89[ASN][1000 genomes]
rs3805652	0.94[CHD][hapmap]
rs55721088	0.91[ASN][1000 genomes]
rs56049336	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57050667	0.94[ASN][1000 genomes]
rs58889726	0.89[ASN][1000 genomes]
rs59674940	0.94[ASN][1000 genomes]
rs60201468	0.94[ASN][1000 genomes]
rs60571728	0.94[ASN][1000 genomes]
rs60975118	0.88[ASN][1000 genomes]
rs6595830	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs6595831	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs6595834	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs6595836	0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs6595837	0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs6860199	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs6864057	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs6886186	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs6887851	0.92[ASN][1000 genomes]
rs6892484	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs6893116	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs6893181	1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs73346331	0.89[ASN][1000 genomes]
rs73784600	0.91[ASN][1000 genomes]
rs73787623	0.88[ASN][1000 genomes]
rs768744	0.92[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs7703313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7708713	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7713044	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7722917	0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs7722950	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7723500	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7725740	0.94[ASN][1000 genomes]
rs7726535	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs9327478	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs981411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17839642	FBN2	cis	lung	GTEx
rs17839642	FBN2	cis	Artery Aorta	GTEx
rs17839642	FBN2	cis	Whole Blood	GTEx
rs17839642	FBN2	cis	multi-tissue	Pritchard
rs17839642	FBN2	cis	Nerve Tibial	GTEx
rs17839642	FBN2	cis	Artery Tibial	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127800400-127845600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:127803400-127839200	Weak transcription	Fetal Stomach	stomach
3	chr5:127806400-127847000	Weak transcription	NHDF-Ad	bronchial
4	chr5:127806600-127839600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:127806600-127839600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:127806600-127839600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:127810800-127839400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr5:127811000-127835200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:127816400-127836600	Weak transcription	Placenta	Placenta
10	chr5:127823000-127839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:127824000-127835800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:127824800-127853800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:127826200-127859800	Weak transcription	NH-A	brain
14	chr5:127827200-127838800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:127827200-127849600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:127827200-127870400	Weak transcription	Fetal Kidney	kidney
17	chr5:127827400-127840200	Weak transcription	Fetal Lung	lung
18	chr5:127827600-127854000	Weak transcription	HUVEC	blood vessel
19	chr5:127827800-127839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:127830200-127834800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:127830400-127839600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:127830800-127834200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:127831200-127834800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:127831400-127833600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:127832000-127833800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:127832000-127839400	Weak transcription	HMEC	breast
27	chr5:127832400-127836600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:127832800-127834200	Enhancers	Fetal Heart	heart
29	chr5:127832800-127836000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:127832800-127837000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:127833000-127833200	ZNF genes & repeats	Fetal Muscle Leg	muscle

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