Variant report

Variant	rs62481903
Chromosome Location	chr7:128280069-128280070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM71F2-1	chr7:128278828-128281168	XLOC_006242
2	lnc-FAM71F2-1	chr7:128278998-128280471	NONHSAT123216
3	lnc-FAM71F2-1	chr7:128278644-128281373	NONHSAT123217

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10273146	0.86[EUR][1000 genomes]
rs10954208	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10954209	0.80[EUR][1000 genomes]
rs10954210	0.82[EUR][1000 genomes]
rs11763357	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532347	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12534956	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12535956	0.81[EUR][1000 genomes]
rs13247422	0.86[EUR][1000 genomes]
rs2003954	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2013189	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2060718	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56403867	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57185253	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58709686	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58781928	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60117311	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61310483	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62481159	0.85[EUR][1000 genomes]
rs62481882	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62481884	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62481943	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62483279	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62483283	0.87[EUR][1000 genomes]
rs62483292	0.81[EUR][1000 genomes]
rs62483312	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6971091	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73723614	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv970938	chr7:128256300-128300276	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv981679	chr7:128278778-128282292	Weak transcription Strong transcription	lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62481903	RP11-274B21.4	cis	lung	GTEx
rs62481903	RP11-274B21.2	cis	Thyroid	GTEx
rs62481903	CICP14	cis	Thyroid	GTEx
rs62481903	RP11-274B21.4	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128237800-128290400	Weak transcription	HepG2	liver
2	chr7:128239200-128287200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:128239200-128296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:128242600-128292800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:128246600-128284800	Weak transcription	Stomach Mucosa	stomach
6	chr7:128249600-128283200	Weak transcription	Hela-S3	cervix
7	chr7:128249600-128285800	Weak transcription	Fetal Heart	heart
8	chr7:128249600-128286800	Weak transcription	HSMMtube	muscle
9	chr7:128249600-128289000	Weak transcription	NHEK	skin
10	chr7:128249600-128293400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:128249600-128295200	Weak transcription	NH-A	brain
12	chr7:128249600-128297600	Weak transcription	HUVEC	blood vessel
13	chr7:128249600-128308400	Weak transcription	HSMM	muscle
14	chr7:128249600-128312200	Weak transcription	Psoas Muscle	Psoas
15	chr7:128249600-128319600	Weak transcription	NHLF	lung
16	chr7:128252200-128287600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:128256800-128288600	Weak transcription	Osteobl	bone
18	chr7:128258600-128287400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:128260000-128296400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr7:128260400-128300600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:128262200-128293200	Weak transcription	Brain Germinal Matrix	brain
22	chr7:128262600-128283800	Weak transcription	Small Intestine	intestine
23	chr7:128263000-128286600	Weak transcription	Fetal Brain Male	brain
24	chr7:128265800-128289000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:128266400-128290400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr7:128267200-128287400	Strong transcription	Fetal Muscle Leg	muscle
27	chr7:128272200-128300000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:128272400-128285800	Weak transcription	Fetal Kidney	kidney
29	chr7:128272400-128290400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:128272400-128290400	Weak transcription	K562	blood
31	chr7:128272400-128292400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr7:128272400-128293200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:128273600-128290600	Weak transcription	Fetal Brain Female	brain
34	chr7:128273800-128283600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:128273800-128291800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr7:128274200-128283800	Weak transcription	GM12878-XiMat	blood
37	chr7:128274200-128296400	Weak transcription	Colonic Mucosa	Colon
38	chr7:128274400-128283800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr7:128274400-128287400	Strong transcription	Liver	Liver
40	chr7:128274600-128291200	Weak transcription	Esophagus	oesophagus
41	chr7:128275600-128287400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr7:128275600-128295000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:128275800-128282600	Strong transcription	Fetal Thymus	thymus
44	chr7:128275800-128289600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:128276000-128287200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr7:128276000-128287600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:128276200-128284400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:128276200-128287400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr7:128277200-128281400	Strong transcription	Thymus	Thymus
50	chr7:128277200-128282400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links