Variant report

Variant	rs3909897
Chromosome Location	chr5:127675355-127675356
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC12A2-5	chr5:127675079-127675679	NONHSAT103661

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10038028	0.86[AMR][1000 genomes]
rs10040416	1.00[ASN][1000 genomes]
rs10041869	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10044959	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10046007	1.00[ASN][1000 genomes]
rs10055617	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10057231	1.00[ASN][1000 genomes]
rs10057405	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057855	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10062686	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063393	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10067405	1.00[ASN][1000 genomes]
rs10070076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10070942	1.00[AFR][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[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077809	1.00[AFR][1000 genomes]
rs10477683	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10477684	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10478806	1.00[AFR][1000 genomes]
rs10478811	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11950890	1.00[ASN][1000 genomes]
rs11951790	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11951921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11952130	1.00[ASN][1000 genomes]
rs11955447	1.00[ASN][1000 genomes]
rs12189448	1.00[CHB][hapmap]
rs13360784	1.00[ASN][1000 genomes]
rs1396477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561006	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17164115	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17608692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17676236	1.00[AFR][1000 genomes]
rs17676260	1.00[AFR][1000 genomes]
rs17676426	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1848501	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1858080	1.00[CHB][hapmap]
rs1978439	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063248	1.00[ASN][1000 genomes]
rs28579194	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28800517	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374748	1.00[JPT][hapmap]
rs3792871	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3816905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4492151	1.00[ASN][1000 genomes]
rs55733883	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56228613	1.00[ASN][1000 genomes]
rs59535791	1.00[ASN][1000 genomes]
rs59820839	1.00[ASN][1000 genomes]
rs6867183	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873360	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6881856	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6883276	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6893195	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes]
rs7356632	1.00[ASN][1000 genomes]
rs7700287	0.83[ASN][1000 genomes]
rs7719113	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7731176	1.00[ASN][1000 genomes]
rs9327476	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989548	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs989549	1.00[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3909897	FBN2	cis	Whole Blood	GTEx
rs3909897	FBN2	cis	Artery Tibial	GTEx
rs3909897	FBN2	cis	lung	GTEx
rs3909897	FBN2	cis	multi-tissue	Pritchard
rs3909897	FBN2	cis	Nerve Tibial	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127638200-127685000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:127657400-127685000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:127658000-127683600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:127659200-127693600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:127659200-127693800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:127660600-127683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:127660600-127687000	Weak transcription	Fetal Brain Female	brain
8	chr5:127661000-127675800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:127661200-127675600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr5:127661200-127683800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:127661200-127693000	Weak transcription	NHLF	lung
12	chr5:127661200-127693600	Strong transcription	Placenta	Placenta
13	chr5:127661800-127683600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:127662000-127681400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:127662400-127675800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:127663200-127675400	Weak transcription	Fetal Intestine Large	intestine
17	chr5:127664600-127678800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:127664600-127682000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:127665400-127676600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:127666800-127676400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr5:127667400-127675600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:127668400-127676800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:127668600-127675600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:127668800-127675800	Strong transcription	Fetal Muscle Leg	muscle
25	chr5:127668800-127681200	Weak transcription	Gastric	stomach
26	chr5:127669800-127677400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:127671000-127676800	Weak transcription	Right Ventricle	heart
28	chr5:127671000-127677200	Weak transcription	Fetal Kidney	kidney
29	chr5:127671800-127681000	Weak transcription	Ovary	ovary
30	chr5:127672000-127746000	Weak transcription	NHDF-Ad	bronchial
31	chr5:127672200-127676600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr5:127672400-127678800	Weak transcription	HMEC	breast
33	chr5:127673000-127675800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr5:127673000-127675800	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr5:127673200-127675600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:127673200-127675600	Strong transcription	NHEK	skin
37	chr5:127673200-127679800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:127673200-127683800	Strong transcription	Fetal Stomach	stomach
39	chr5:127673400-127680000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:127673400-127681200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:127673800-127677000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:127673800-127706400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:127674000-127680800	Weak transcription	HUVEC	blood vessel
44	chr5:127674200-127675600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:127674200-127676600	Weak transcription	NH-A	brain
46	chr5:127674200-127678000	Genic enhancers	Fetal Heart	heart
47	chr5:127674400-127675600	Strong transcription	Fetal Intestine Small	intestine
48	chr5:127674600-127675600	Enhancers	Left Ventricle	heart
49	chr5:127674600-127678200	Weak transcription	Fetal Lung	lung
50	chr5:127674800-127675600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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