Variant report

Variant	rs7777453
Chromosome Location	chr7:79089737-79089738
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAGI2-1	chr7:79088353-79093892	ENSG00000249657
2	lnc-MAGI2-1	chr7:79088787-79091858	XLOC_006507
3	lnc-GNAI1-2	chr7:79088852-79093061	ENSG00000234456.2
4	lnc-GNAI1-2	chr7:79088852-79089916	NONHSAT121716
5	lnc-GNAI1-2	chr7:79088852-79096786	ENSG00000234456.3
6	lnc-GNAI1-2	chr7:79088852-79090496	NONHSAT121718

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10226316	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10226488	0.98[ASN][1000 genomes]
rs10233817	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10238639	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10239130	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10251407	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10255409	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10258595	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10260483	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs10808188	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706177	0.88[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2214804	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2365421	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2886360	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4730832	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs4730835	0.90[EUR][1000 genomes]
rs4730857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730874	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730878	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4730892	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6466663	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466670	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6957474	0.97[YRI][hapmap];0.99[AFR][1000 genomes]
rs6974444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7801286	0.86[EUR][1000 genomes]
rs7802400	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7808033	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7810711	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7810716	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7812062	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv888516	chr7:79086317-79221707	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79084200-79091200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:79084400-79095000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:79084400-79102200	Weak transcription	Left Ventricle	heart
4	chr7:79084600-79101000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:79084800-79091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:79084800-79100800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr7:79084800-79102800	Weak transcription	HSMM	muscle
8	chr7:79085000-79090400	Weak transcription	Lung	lung
9	chr7:79085000-79098600	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:79085000-79099600	Weak transcription	Fetal Stomach	stomach
11	chr7:79085200-79091800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:79085800-79089800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:79085800-79090800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:79085800-79095400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:79085800-79098000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:79086000-79099800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr7:79086200-79090400	Weak transcription	Fetal Kidney	kidney
18	chr7:79086200-79093800	Weak transcription	Brain Substantia Nigra	brain
19	chr7:79086400-79090600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:79086600-79099600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:79086600-79100600	Weak transcription	Brain Anterior Caudate	brain
22	chr7:79086600-79101000	Weak transcription	Brain Angular Gyrus	brain
23	chr7:79086600-79101400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:79086600-79104200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr7:79087000-79090000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:79087600-79099800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:79087800-79090400	Strong transcription	HUVEC	blood vessel
28	chr7:79087800-79093400	Weak transcription	Brain Hippocampus Middle	brain
29	chr7:79087800-79099800	Weak transcription	Fetal Lung	lung
30	chr7:79088000-79091800	Weak transcription	Ovary	ovary
31	chr7:79088000-79109600	Weak transcription	Aorta	Aorta
32	chr7:79088200-79089800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:79088600-79092200	Enhancers	HepG2	liver
34	chr7:79088800-79090000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:79088800-79090200	Strong transcription	NHDF-Ad	bronchial
36	chr7:79088800-79090800	Enhancers	A549	lung
37	chr7:79088800-79093400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:79089000-79089800	Strong transcription	Liver	Liver
39	chr7:79089000-79098800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr7:79089000-79102800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:79089200-79090200	Genic enhancers	Osteobl	bone
42	chr7:79089200-79098000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr7:79089200-79100200	Weak transcription	Adipose Nuclei	Adipose
44	chr7:79089200-79109600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:79089400-79089800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:79089400-79093400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:79089400-79093800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:79089400-79101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:79089600-79089800	Genic enhancers	Colon Smooth Muscle	Colon
50	chr7:79089600-79090200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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