Variant report

Variant	rs7783388
Chromosome Location	chr7:79085343-79085344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr7:79085178-79085526	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr7:79085294-79086003	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:79085147-79086117	PFSK-1	brain:	n/a	n/a
4	CTCF	chr7:79085220-79085370	HEEpiC	esophagus:	n/a	n/a
5	ZNF263	chr7:79081100-79085959	HEK293-T-REx	kidney:	n/a	chr7:79083163-79083172 chr7:79081619-79081628 chr7:79085459-79085468 chr7:79083175-79083184 chr7:79083164-79083185 chr7:79082994-79083003 chr7:79081426-79081435
6	POLR2A	chr7:79084718-79085614	PFSK-1	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:79085293-79085343	HPAEpiC	pulmonary alveolar:	n/a
2	chr7:79085293-79085343	U87	brain:	n/a
3	chr7:79085293-79085343	HNPCEpiC	eye:	n/a
4	chr7:79085293-79085343	HRCEpiC	kidney:	n/a
5	chr7:79085293-79085343	ovcar-3	ovarian:	n/a
6	chr7:79085293-79085343	K562	blood:	n/a
7	chr7:79085293-79085343	Jurkat	blood:	n/a
8	chr7:79085293-79085343	AG04449	skin:	fetal
9	chr7:79085293-79085343	GM12892	blood:	n/a
10	chr7:79085293-79085343	HL-60	blood:	n/a
11	chr7:79085293-79085343	AG10803	skin:	n/a
12	chr7:79085293-79085343	HCT-116	colon:	n/a
13	chr7:79085293-79085343	HUVEC	blood vessel:	n/a
14	chr7:79085293-79085343	AG04450	lung:	fetal
15	chr7:79085293-79085343	Hepatocyte	liver:	n/a
16	chr7:79085293-79085343	GM12891	blood:	n/a
17	chr7:79085293-79085343	NHBE	bronchial:	n/a
18	chr7:79085293-79085343	AoSMC	blood vessel:	n/a
19	chr7:79085293-79085343	Caco-2	colon:	n/a
20	chr7:79085293-79085343	H1-hESC	embryonic stem cell:	embryo
21	chr7:79085293-79085343	PANC-1	pancreas:	n/a
22	chr7:79085293-79085343	NH-A	brain:	n/a
23	chr7:79085293-79085343	SKMC	muscle:	n/a
24	chr7:79085293-79085343	GM19239	blood:	n/a
25	chr7:79085293-79085343	BE2_C	brain:	n/a
26	chr7:79085293-79085343	LNCaP	prostate:	n/a
27	chr7:79085293-79085343	HEK293	kidney:	embryo
28	chr7:79085293-79085343	NT2-D1	testis:	n/a
29	chr7:79085293-79085343	HMEC	breast:	n/a
30	chr7:79085293-79085343	AG09319	gingival:	n/a
31	chr7:79085293-79085343	HRE	kidney:	n/a
32	chr7:79085293-79085343	HCF	heart:	n/a
33	chr7:79085293-79085343	RPTEC	kidney:	n/a
34	chr7:79085293-79085343	SK-N-MC	brain:	n/a
35	chr7:79085293-79085343	ECC-1	luminal epithelium:	n/a
36	chr7:79085293-79085343	MCF-7	breast:	n/a
37	chr7:79085293-79085343	BJ	skin:	n/a
38	chr7:79085293-79085343	PFSK-1	brain:	n/a
39	chr7:79085293-79085343	HCPEpiC	choroid plexus:	n/a
40	chr7:79085293-79085343	HRPEpiC	eye:	n/a
41	chr7:79085293-79085343	IMR90	lung:	fetal
42	chr7:79085293-79085343	HEEpiC	esophagus:	n/a
43	chr7:79085293-79085343	CMK	blood:	n/a
44	chr7:79085293-79085343	SAEC	small airway:	n/a
45	chr7:79085293-79085343	GM06990	blood:	n/a
46	chr7:79085293-79085343	HCM	heart:	n/a
47	chr7:79085293-79085343	NHDF-neo	bronchial:	n/a
48	chr7:79085293-79085343	HepG2	liver:	n/a
49	chr7:79085293-79085343	ProgFib	skin:	n/a
50	chr7:79085293-79085343	SK-N-SH_RA	brain:	n/a

No data

Variant related genes	Relation type
MAGI2-AS3	TF binding region
MAGI2	TF binding region
MAGI2-AS3	CpG island
MAGI2	CpG island

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10252126	0.86[MEX][hapmap]
rs10259665	0.86[JPT][hapmap]
rs10260483	0.86[MEX][hapmap]
rs10261468	0.85[JPT][hapmap]
rs1034796	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1859596	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2158706	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2269989	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2269990	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2269992	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4727868	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4727869	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4730830	0.90[JPT][hapmap]
rs726655	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7791832	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7802883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2764028	chr7:78874740-79112630	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv888515	chr7:78987060-79221707	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv427792	chr7:79039802-79253373	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv970902	chr7:79046674-79175610	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7783388	LOC402560	cis	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79081400-79086200	Active TSS	Fetal Kidney	kidney
2	chr7:79084000-79085600	Flanking Active TSS	Colon Smooth Muscle	Colon
3	chr7:79084000-79085800	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr7:79084000-79086000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:79084200-79085400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:79084200-79085400	Weak transcription	Esophagus	oesophagus
7	chr7:79084200-79091200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:79084400-79085400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:79084400-79085400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:79084400-79085400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
11	chr7:79084400-79085400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:79084400-79085800	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr7:79084400-79086000	Weak transcription	Fetal Brain Male	brain
14	chr7:79084400-79086200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:79084400-79086200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:79084400-79088200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:79084400-79089000	Weak transcription	NH-A	brain
18	chr7:79084400-79095000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:79084400-79102200	Weak transcription	Left Ventricle	heart
20	chr7:79084600-79085400	Enhancers	Ovary	ovary
21	chr7:79084600-79085800	Enhancers	Liver	Liver
22	chr7:79084600-79085800	Enhancers	Rectal Smooth Muscle	rectum
23	chr7:79084600-79085800	Enhancers	Spleen	Spleen
24	chr7:79084600-79101000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:79084800-79085400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:79084800-79085400	Weak transcription	Aorta	Aorta
27	chr7:79084800-79085600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr7:79084800-79085800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr7:79084800-79085800	Enhancers	NHDF-Ad	bronchial
30	chr7:79084800-79086000	Enhancers	Right Atrium	heart
31	chr7:79084800-79086000	Transcr. at gene 5' and 3'	NHLF	lung
32	chr7:79084800-79086600	Enhancers	Brain Cingulate Gyrus	brain
33	chr7:79084800-79087000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:79084800-79087600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:79084800-79091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:79084800-79100800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:79084800-79102800	Weak transcription	HSMM	muscle
38	chr7:79085000-79085400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:79085000-79085600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr7:79085000-79085800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr7:79085000-79085800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr7:79085000-79086200	Strong transcription	HUVEC	blood vessel
43	chr7:79085000-79086400	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr7:79085000-79086600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:79085000-79086600	Enhancers	Brain Angular Gyrus	brain
46	chr7:79085000-79086600	Enhancers	Brain Anterior Caudate	brain
47	chr7:79085000-79086600	Enhancers	Brain Hippocampus Middle	brain
48	chr7:79085000-79086600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:79085000-79087000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:79085000-79087400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links