Variant report

Variant	rs989548
Chromosome Location	chr5:127740383-127740384
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10040416	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044959	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10046007	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10057231	0.86[AMR][1000 genomes];0.98[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[ASW][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs10059301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059368	1.00[AFR][1000 genomes]
rs10062686	1.00[ASN][1000 genomes]
rs10063393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063914	1.00[AFR][1000 genomes]
rs10067405	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067859	0.80[EUR][1000 genomes]
rs10070076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071920	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074194	1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074198	0.92[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];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10478811	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs10519994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950890	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952130	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955447	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13355538	1.00[AFR][1000 genomes]
rs13360784	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561006	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17164083	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs17164115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17608692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17615636	1.00[AFR][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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1978439	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2063248	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617614	1.00[AFR][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]
rs3792873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816905	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3909897	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs4492151	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55733883	1.00[ASN][1000 genomes]
rs56228613	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59535791	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59820839	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867183	1.00[ASN][1000 genomes]
rs6873360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6881856	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6883276	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893195	1.00[JPT][hapmap]
rs7356632	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7700287	0.83[ASN][1000 genomes]
rs7719113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731176	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327476	1.00[ASN][1000 genomes]
rs968008	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs989549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs989548	FBN2	cis	Artery Tibial	GTEx
rs989548	FBN2	cis	lung	GTEx
rs989548	FBN2	cis	Nerve Tibial	GTEx
rs989548	FBN2	cis	Thyroid	GTEx
rs989548	FBN2	cis	Artery Aorta	GTEx
rs989548	FBN2	cis	Whole Blood	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127672000-127746000	Weak transcription	NHDF-Ad	bronchial
2	chr5:127675600-127742200	Weak transcription	Fetal Intestine Small	intestine
3	chr5:127686000-127742000	Weak transcription	A549	lung
4	chr5:127704800-127741800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:127714600-127743000	Weak transcription	HMEC	breast
6	chr5:127716600-127744800	Weak transcription	Fetal Kidney	kidney
7	chr5:127725400-127743000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:127725600-127743800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:127725800-127743400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:127725800-127765600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:127726000-127745000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:127727800-127740600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:127728400-127741800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:127728400-127744200	Weak transcription	NH-A	brain
15	chr5:127729000-127742200	Weak transcription	Ovary	ovary
16	chr5:127729200-127740600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr5:127731400-127747000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:127731800-127740600	Weak transcription	Fetal Stomach	stomach
19	chr5:127733200-127744400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:127733800-127744200	Weak transcription	Right Ventricle	heart
21	chr5:127734400-127742600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:127736400-127745000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:127737800-127742200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:127738600-127740800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr5:127738800-127740600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:127739200-127742400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:127739200-127743400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:127739200-127744800	Weak transcription	HUVEC	blood vessel
29	chr5:127739200-127789000	Weak transcription	Left Ventricle	heart
30	chr5:127739400-127740600	Strong transcription	Placenta	Placenta
31	chr5:127739400-127759800	Weak transcription	Fetal Lung	lung
32	chr5:127739600-127740400	Weak transcription	NHEK	skin
33	chr5:127739600-127744200	Weak transcription	Fetal Brain Male	brain
34	chr5:127739800-127741400	Weak transcription	Fetal Heart	heart
35	chr5:127739800-127742600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:127739800-127744600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr5:127740000-127740400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:127740000-127740600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:127740000-127740800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:127740000-127740800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:127740000-127743800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:127740000-127744400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:127740200-127741200	Strong transcription	Fetal Muscle Leg	muscle
44	chr5:127740200-127744400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:127740200-127744400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links