Variant report

Variant	rs3792873
Chromosome Location	chr5:127790071-127790072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10040416	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044959	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10046007	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10057231	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057405	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10057855	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10059301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062686	1.00[ASN][1000 genomes]
rs10063393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067405	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071920	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074194	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074198	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076728	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10477683	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10477684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10478811	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10519994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520003	0.81[EUR][1000 genomes]
rs11950890	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952130	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955447	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13360784	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1561006	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17164115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17608692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17676426	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1848501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1978439	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2063248	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28579194	1.00[ASN][1000 genomes]
rs28800517	1.00[ASN][1000 genomes]
rs374748	1.00[JPT][hapmap]
rs3792871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3816905	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3909897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4492151	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55733883	1.00[ASN][1000 genomes]
rs55944506	0.81[EUR][1000 genomes]
rs56228613	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58143160	0.81[EUR][1000 genomes]
rs58295967	0.81[EUR][1000 genomes]
rs59535791	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59820839	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60324229	0.81[EUR][1000 genomes]
rs6867183	1.00[ASN][1000 genomes]
rs6873360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6881856	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6883276	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893195	1.00[JPT][hapmap]
rs7356632	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764369	0.81[EUR][1000 genomes]
rs7700287	0.83[ASN][1000 genomes]
rs7719113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731176	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs892864	0.81[EUR][1000 genomes]
rs9327476	1.00[ASN][1000 genomes]
rs968008	0.81[EUR][1000 genomes]
rs989548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3792873	FBN2	cis	Artery Tibial	GTEx
rs3792873	FBN2	cis	Nerve Tibial	GTEx
rs3792873	FBN2	cis	lung	GTEx
rs3792873	FBN2	cis	Artery Aorta	GTEx
rs3792873	FBN2	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127760600-127791400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:127772600-127807600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:127772800-127799800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:127773000-127809400	Weak transcription	HMEC	breast
5	chr5:127773400-127830000	Weak transcription	NHEK	skin
6	chr5:127777200-127793000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:127779400-127807400	Weak transcription	Fetal Kidney	kidney
8	chr5:127780400-127806400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:127780800-127805400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:127782400-127796200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:127784000-127791000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:127784000-127795000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:127784000-127826800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:127784800-127792000	Weak transcription	Placenta	Placenta
15	chr5:127786000-127797800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:127786400-127791600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:127786400-127799000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:127787000-127793000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:127787200-127791200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:127787200-127798200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:127787400-127806200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:127788600-127790600	Enhancers	Fetal Lung	lung
23	chr5:127788800-127792400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:127788800-127810600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:127789000-127790600	Genic enhancers	Fetal Heart	heart
26	chr5:127789000-127791000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:127789000-127793200	Enhancers	Fetal Stomach	stomach
28	chr5:127789400-127794200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:127789600-127802800	Weak transcription	Left Ventricle	heart
30	chr5:127790000-127790800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr5:127790000-127791000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:127790000-127791200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:127790000-127791400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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