Variant report

Variant	rs1141114
Chromosome Location	chr7:30616247-30616248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCT-1	chr7:30616180-30616326	ENSG00000196295.5
2	lnc-GGCT-1	chr7:30616180-30616358	ENSG00000196295.5
3	lnc-GGCT-1	chr7:30616180-30616326	ENSG00000196295.5
4	lnc-GGCT-1	chr7:30616180-30616476	NONHSAT119880
5	lnc-GGCT-1	chr7:30616180-30616326	NONHSAT119889

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10227133	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10232372	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233132	0.81[ASN][1000 genomes]
rs10237725	0.85[EUR][1000 genomes]
rs10239660	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10243040	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249885	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10265589	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10480088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074373	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951271	0.83[ASN][1000 genomes]
rs11761080	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532057	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12533961	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13228758	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468402	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1558064	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16875282	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16875285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009662	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214837	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240401	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267710	0.84[ASN][1000 genomes]
rs2270025	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391870	0.81[EUR][1000 genomes]
rs3779250	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3807632	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722992	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722999	0.86[ASN][1000 genomes]
rs6462211	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947982	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6970688	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970807	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9648369	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1024458	chr7:30601877-30649659	Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3417912	chr7:30612318-30619224	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1141114	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs1141114	AC005154.6	cis	Nerve Tibial	GTEx
rs1141114	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs1141114	AC005154.6	cis	Artery Tibial	GTEx
rs1141114	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs1141114	AC005154.6	cis	lung	GTEx
rs1141114	AC005154.6	cis	Thyroid	GTEx
rs1141114	AC005154.6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
2	chr7:30591200-30633400	Weak transcription	Psoas Muscle	Psoas
3	chr7:30597400-30633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:30597600-30624400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:30598400-30623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:30599400-30617400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:30601800-30633000	Weak transcription	Hela-S3	cervix
8	chr7:30603200-30621000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:30603200-30628400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:30604600-30617800	Weak transcription	Right Ventricle	heart
11	chr7:30604600-30624400	Weak transcription	Gastric	stomach
12	chr7:30605600-30628200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:30607000-30617400	Weak transcription	Esophagus	oesophagus
14	chr7:30607000-30617600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:30607000-30633400	Weak transcription	Fetal Kidney	kidney
16	chr7:30607600-30617400	Weak transcription	Brain Angular Gyrus	brain
17	chr7:30608200-30617400	Weak transcription	NHLF	lung
18	chr7:30608200-30618400	Weak transcription	Brain Substantia Nigra	brain
19	chr7:30608400-30616600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:30608400-30617400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:30608400-30617400	Weak transcription	Pancreas	Pancrea
22	chr7:30608400-30617400	Weak transcription	Spleen	Spleen
23	chr7:30608400-30617600	Weak transcription	Brain Anterior Caudate	brain
24	chr7:30608600-30617400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:30608600-30618000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr7:30609800-30621400	Weak transcription	K562	blood
27	chr7:30610400-30617400	Weak transcription	Lung	lung
28	chr7:30610400-30617400	Weak transcription	Thymus	Thymus
29	chr7:30610600-30617400	Weak transcription	Fetal Intestine Small	intestine
30	chr7:30610600-30617400	Weak transcription	Small Intestine	intestine
31	chr7:30610600-30617400	Weak transcription	NH-A	brain
32	chr7:30612000-30618600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
33	chr7:30612200-30617400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr7:30612200-30618000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:30612200-30618800	Strong transcription	Placenta	Placenta
36	chr7:30612200-30625000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:30612200-30625600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:30612200-30627000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:30612800-30619000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
40	chr7:30612800-30628600	Weak transcription	Stomach Mucosa	stomach
41	chr7:30613000-30618800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:30613200-30617200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:30613200-30619000	Strong transcription	Osteobl	bone
44	chr7:30613200-30619600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
45	chr7:30613600-30617400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr7:30613600-30619200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr7:30613800-30617200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr7:30613800-30617400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr7:30613800-30619400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
50	chr7:30614000-30617200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links