Variant report

Variant	rs38486
Chromosome Location	chr7:30612447-30612448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr7:30612115-30612479	A549	lung:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCT-1	chr7:30611839-30614499	NONHSAT119880

Variant related genes	Relation type
ENSG00000196295	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1049402	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1986756	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2529437	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2709787	0.98[ASN][1000 genomes]
rs2709809	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38484	0.82[ASN][1000 genomes]
rs38485	0.96[ASN][1000 genomes]
rs38487	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38488	0.99[ASN][1000 genomes]
rs38489	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38493	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38494	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38495	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38497	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38498	0.99[ASN][1000 genomes]
rs973002	0.81[ASN][1000 genomes]
rs975537	0.86[EUR][1000 genomes];0.91[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs38486	AC005154.6	cis	lung	GTEx
rs38486	AC005154.6	cis	Heart Left Ventricle	GTEx
rs38486	AC005154.8	cis	Whole Blood	GTEx
rs38486	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38486	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38486	AC005154.6	cis	Muscle Skeletal	GTEx
rs38486	AC005154.6	cis	Thyroid	GTEx
rs38486	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38486	AC005154.6	cis	Whole Blood	GTEx
rs38486	AC005154.6	cis	Stomach	GTEx
rs38486	AC005154.6	cis	Nerve Tibial	GTEx
rs38486	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38486	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38486	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38486	AC005154.6	cis	Artery Tibial	GTEx
rs38486	AC005154.6	cis	Artery Aorta	GTEx

Chromatin state (count:114 , 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	chr7:30596600-30614400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:30597400-30633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:30597600-30624400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:30598400-30623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:30599400-30617400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr7:30601800-30633000	Weak transcription	Hela-S3	cervix
9	chr7:30602800-30615400	Weak transcription	Fetal Brain Female	brain
10	chr7:30602800-30616200	Weak transcription	Fetal Brain Male	brain
11	chr7:30603200-30621000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:30603200-30628400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:30603600-30612600	Weak transcription	Colonic Mucosa	Colon
14	chr7:30604000-30612800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:30604000-30613000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:30604000-30613600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr7:30604000-30615000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:30604000-30615200	Weak transcription	HepG2	liver
19	chr7:30604000-30615200	Weak transcription	NHEK	skin
20	chr7:30604000-30615400	Weak transcription	NHDF-Ad	bronchial
21	chr7:30604200-30613400	Weak transcription	HUVEC	blood vessel
22	chr7:30604600-30617800	Weak transcription	Right Ventricle	heart
23	chr7:30604600-30624400	Weak transcription	Gastric	stomach
24	chr7:30605600-30628200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:30607000-30614400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:30607000-30617400	Weak transcription	Esophagus	oesophagus
27	chr7:30607000-30617600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr7:30607000-30633400	Weak transcription	Fetal Kidney	kidney
29	chr7:30607600-30617400	Weak transcription	Brain Angular Gyrus	brain
30	chr7:30608200-30617400	Weak transcription	NHLF	lung
31	chr7:30608200-30618400	Weak transcription	Brain Substantia Nigra	brain
32	chr7:30608400-30613000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:30608400-30613600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:30608400-30615600	Weak transcription	Fetal Lung	lung
35	chr7:30608400-30616600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:30608400-30617400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:30608400-30617400	Weak transcription	Pancreas	Pancrea
38	chr7:30608400-30617400	Weak transcription	Spleen	Spleen
39	chr7:30608400-30617600	Weak transcription	Brain Anterior Caudate	brain
40	chr7:30608600-30612600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:30608600-30612600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr7:30608600-30613200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr7:30608600-30617400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr7:30608600-30618000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:30608800-30612600	Weak transcription	Fetal Intestine Large	intestine
46	chr7:30608800-30613400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:30609000-30613200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr7:30609200-30612800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr7:30609400-30613000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr7:30609800-30614600	Strong transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links