Variant report

Variant	rs1978439
Chromosome Location	chr5:127645329-127645330
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10038028	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10040416	1.00[ASN][1000 genomes]
rs10041869	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10044959	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10046007	1.00[ASN][1000 genomes]
rs10055617	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10057231	1.00[ASN][1000 genomes]
rs10057405	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057855	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059301	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10062686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063393	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10067405	1.00[ASN][1000 genomes]
rs10070076	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10071920	1.00[ASN][1000 genomes]
rs10074194	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10074198	1.00[ASN][1000 genomes]
rs10076728	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477683	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477684	1.00[JPT][hapmap]
rs10478811	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519994	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11950890	1.00[ASN][1000 genomes]
rs11951790	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11951921	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11952130	1.00[ASN][1000 genomes]
rs11955447	1.00[ASN][1000 genomes]
rs13360784	1.00[ASN][1000 genomes]
rs1396477	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1561006	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17164115	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17608692	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17676426	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1848501	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1858080	1.00[JPT][hapmap]
rs2063248	1.00[ASN][1000 genomes]
rs28579194	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28800517	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374748	1.00[JPT][hapmap]
rs3792871	1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792873	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3816905	1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3909897	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4492151	1.00[ASN][1000 genomes]
rs55733883	1.00[ASN][1000 genomes]
rs56228613	1.00[ASN][1000 genomes]
rs59535791	1.00[ASN][1000 genomes]
rs59820839	1.00[ASN][1000 genomes]
rs6867183	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6873360	1.00[JPT][hapmap]
rs6881856	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6883276	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6893195	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7356632	1.00[ASN][1000 genomes]
rs7719113	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7731176	1.00[ASN][1000 genomes]
rs9327476	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989548	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs989549	1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830482	chr5:127475398-127665377	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv599697	chr5:127563563-127731210	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv830483	chr5:127595570-127705124	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1978439	FBN2	cis	Thyroid	GTEx
rs1978439	FBN2	cis	Whole Blood	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127589000-127670200	Weak transcription	NHDF-Ad	bronchial
2	chr5:127612800-127662400	Weak transcription	HUVEC	blood vessel
3	chr5:127614600-127661000	Weak transcription	Fetal Kidney	kidney
4	chr5:127622800-127662000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:127624600-127663600	Weak transcription	A549	lung
6	chr5:127624800-127648000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:127625000-127662200	Weak transcription	Fetal Intestine Large	intestine
8	chr5:127626000-127664400	Weak transcription	Right Ventricle	heart
9	chr5:127626600-127664200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:127634400-127656200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:127635200-127646600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr5:127635600-127645600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:127635600-127654800	Strong transcription	Placenta	Placenta
14	chr5:127636200-127648000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:127636200-127648800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr5:127636600-127661800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:127636800-127647800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:127638200-127645800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:127638200-127685000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:127640000-127645600	Weak transcription	Osteobl	bone
21	chr5:127640000-127647000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:127640200-127661400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:127640400-127647600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:127640400-127656200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:127640600-127662000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:127640800-127646800	Weak transcription	Fetal Stomach	stomach
27	chr5:127641400-127647000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:127641400-127648200	Weak transcription	Left Ventricle	heart
29	chr5:127641400-127649000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:127641400-127664000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:127641600-127646800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:127641600-127650600	Weak transcription	NHEK	skin
33	chr5:127641600-127661800	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:127641800-127660200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:127643000-127647400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:127644400-127647600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:127644600-127647400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:127644600-127647600	Strong transcription	HMEC	breast
39	chr5:127644600-127648600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:127645000-127645600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:127645000-127646400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:127645000-127646800	Weak transcription	Fetal Lung	lung
43	chr5:127645000-127662400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr5:127645200-127651000	Weak transcription	Fetal Heart	heart
45	chr5:127645200-127661200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:127645200-127661400	Weak transcription	NH-A	brain
47	chr5:127645200-127662400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:127645200-127664200	Weak transcription	Ovary	ovary

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