Variant report

Variant	rs38488
Chromosome Location	chr7:30617474-30617475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:30617391-30617571	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCT-1	chr7:30617128-30617707	ENSG00000236455.2
2	lnc-GGCT-1	chr7:30617201-30617707	ENSG00000196295.5
3	lnc-GGCT-1	chr7:30617165-30617709	NONHSAT119880
4	lnc-GGCT-1	chr7:30617082-30617707	NONHSAT119914
5	lnc-GGCT-1	chr7:30617173-30617707	NONHSAT119916
6	lnc-GGCT-1	chr7:30617113-30617707	NONHSAT119915
7	lnc-GGCT-1	chr7:30617281-30617707	NONHSAT119918

No data

Variant related genes	Relation type
ENSG00000196295	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1003929	0.89[MEX][hapmap]
rs1049402	0.82[CEU][hapmap];0.96[ASN][1000 genomes]
rs1986756	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2014663	0.89[MEX][hapmap]
rs2270007	0.88[EUR][1000 genomes]
rs2529437	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2709787	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2709809	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs38417	0.86[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs38419	0.87[EUR][1000 genomes]
rs38420	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs38427	0.87[EUR][1000 genomes]
rs38430	0.83[TSI][hapmap]
rs38433	0.83[TSI][hapmap]
rs38434	0.83[TSI][hapmap]
rs38435	0.86[EUR][1000 genomes]
rs38436	0.86[EUR][1000 genomes]
rs38437	0.86[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs38440	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs38447	0.86[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs38448	0.88[EUR][1000 genomes]
rs38450	0.93[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs38452	0.88[EUR][1000 genomes]
rs38456	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs38458	0.81[EUR][1000 genomes]
rs38461	0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs38462	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs38464	0.83[EUR][1000 genomes]
rs38467	0.82[CHD][hapmap]
rs38468	0.82[CHD][hapmap]
rs38471	0.82[CHD][hapmap]
rs38473	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs38474	0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs38478	0.93[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs38481	0.87[EUR][1000 genomes]
rs38483	0.87[EUR][1000 genomes]
rs38484	0.81[ASN][1000 genomes]
rs38485	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38486	0.99[ASN][1000 genomes]
rs38487	0.82[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38489	0.99[ASN][1000 genomes]
rs38493	0.99[ASN][1000 genomes]
rs38494	0.99[ASN][1000 genomes]
rs38495	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs38497	0.99[ASN][1000 genomes]
rs38498	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973002	0.86[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs975537	0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.89[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
rs38488	AC005154.6	cis	Heart Left Ventricle	GTEx
rs38488	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38488	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38488	LOC401320	cis	uninvolved skin	skin_eQTL
rs38488	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38488	AC005154.6	cis	Nerve Tibial	GTEx
rs38488	AC005154.8	cis	Whole Blood	GTEx
rs38488	AC005154.6	cis	Stomach	GTEx
rs38488	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38488	AC005154.6	cis	Thyroid	GTEx
rs38488	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38488	AC005154.6	cis	Artery Aorta	GTEx
rs38488	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38488	AC005154.6	cis	Muscle Skeletal	GTEx
rs38488	AC005154.6	cis	Artery Tibial	GTEx
rs38488	AC005154.6	cis	lung	GTEx

Chromatin state (count:117 , 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	chr7:30601800-30633000	Weak transcription	Hela-S3	cervix
7	chr7:30603200-30621000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:30603200-30628400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:30604600-30617800	Weak transcription	Right Ventricle	heart
10	chr7:30604600-30624400	Weak transcription	Gastric	stomach
11	chr7:30605600-30628200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:30607000-30617600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr7:30607000-30633400	Weak transcription	Fetal Kidney	kidney
14	chr7:30608200-30618400	Weak transcription	Brain Substantia Nigra	brain
15	chr7:30608400-30617600	Weak transcription	Brain Anterior Caudate	brain
16	chr7:30608600-30618000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:30609800-30621400	Weak transcription	K562	blood
18	chr7:30612000-30618600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
19	chr7:30612200-30618000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:30612200-30618800	Strong transcription	Placenta	Placenta
21	chr7:30612200-30625000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:30612200-30625600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:30612200-30627000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:30612800-30619000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
25	chr7:30612800-30628600	Weak transcription	Stomach Mucosa	stomach
26	chr7:30613000-30618800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:30613200-30619000	Strong transcription	Osteobl	bone
28	chr7:30613200-30619600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
29	chr7:30613600-30619200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr7:30613800-30619400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
31	chr7:30614000-30617600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr7:30614000-30619400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
33	chr7:30614000-30620200	Weak transcription	Aorta	Aorta
34	chr7:30614000-30623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr7:30614000-30633200	Weak transcription	HUVEC	blood vessel
36	chr7:30614200-30617600	Weak transcription	Colon Smooth Muscle	Colon
37	chr7:30614400-30617600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
38	chr7:30614400-30619400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:30614400-30619400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:30614600-30617600	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:30614600-30617600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr7:30614600-30617800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:30614600-30617800	Weak transcription	Colonic Mucosa	Colon
44	chr7:30615200-30618000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:30615200-30618600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
46	chr7:30615400-30617600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:30615400-30617600	Weak transcription	NHEK	skin
48	chr7:30615400-30619000	Strong transcription	Adipose Nuclei	Adipose
49	chr7:30615400-30619200	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr7:30615600-30633200	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links