Variant report

Variant	rs4730857
Chromosome Location	chr7:79085543-79085544
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	POLR2A	chr7:79085294-79086003	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:79085147-79086117	PFSK-1	brain:	n/a	n/a
3	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
4	POLR2A	chr7:79084718-79085614	PFSK-1	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAGI2-1	chr7:79085481-79085594	ENSG00000249657

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

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10226316	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10226488	0.97[ASN][1000 genomes]
rs10231884	0.88[MEX][hapmap]
rs10233817	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10238639	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10239130	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10251407	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10255409	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10258595	0.96[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10808188	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706177	0.88[CEU][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2214804	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2365421	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2886360	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4730832	0.87[CEU][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4730835	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4730838	0.83[TSI][hapmap]
rs4730874	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4730878	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4730892	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6466663	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6466670	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6974444	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7777453	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7801286	0.87[EUR][1000 genomes]
rs7802400	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808033	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7810711	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7810716	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7812062	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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
rs4730857	LOC402560	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 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	chr7:79084200-79091200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:79084400-79085800	Flanking Active TSS	Brain Substantia Nigra	brain
7	chr7:79084400-79086000	Weak transcription	Fetal Brain Male	brain
8	chr7:79084400-79086200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:79084400-79086200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:79084400-79088200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:79084400-79089000	Weak transcription	NH-A	brain
12	chr7:79084400-79095000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:79084400-79102200	Weak transcription	Left Ventricle	heart
14	chr7:79084600-79085800	Enhancers	Liver	Liver
15	chr7:79084600-79085800	Enhancers	Rectal Smooth Muscle	rectum
16	chr7:79084600-79085800	Enhancers	Spleen	Spleen
17	chr7:79084600-79101000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:79084800-79085600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:79084800-79085800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr7:79084800-79085800	Enhancers	NHDF-Ad	bronchial
21	chr7:79084800-79086000	Enhancers	Right Atrium	heart
22	chr7:79084800-79086000	Transcr. at gene 5' and 3'	NHLF	lung
23	chr7:79084800-79086600	Enhancers	Brain Cingulate Gyrus	brain
24	chr7:79084800-79087000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:79084800-79087600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:79084800-79091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:79084800-79100800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:79084800-79102800	Weak transcription	HSMM	muscle
29	chr7:79085000-79085600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr7:79085000-79085800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr7:79085000-79085800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr7:79085000-79086200	Strong transcription	HUVEC	blood vessel
33	chr7:79085000-79086400	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr7:79085000-79086600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:79085000-79086600	Enhancers	Brain Angular Gyrus	brain
36	chr7:79085000-79086600	Enhancers	Brain Anterior Caudate	brain
37	chr7:79085000-79086600	Enhancers	Brain Hippocampus Middle	brain
38	chr7:79085000-79086600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:79085000-79087000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:79085000-79087400	Weak transcription	HSMMtube	muscle
41	chr7:79085000-79087800	Weak transcription	Right Ventricle	heart
42	chr7:79085000-79087800	Enhancers	HepG2	liver
43	chr7:79085000-79088800	Weak transcription	Fetal Brain Female	brain
44	chr7:79085000-79089000	Weak transcription	Fetal Heart	heart
45	chr7:79085000-79090400	Weak transcription	Lung	lung
46	chr7:79085000-79098600	Weak transcription	Fetal Muscle Leg	muscle
47	chr7:79085000-79099600	Weak transcription	Fetal Stomach	stomach
48	chr7:79085200-79085600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:79085200-79085800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:79085200-79085800	Genic enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links