Variant report

Variant	rs980354
Chromosome Location	chr7:79095276-79095277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAGI2-1	chr7:79093975-79096779	ENSG00000249657
2	lnc-GNAI1-2	chr7:79088852-79096786	ENSG00000234456.3

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1017037	1.00[ASN][1000 genomes]
rs1034797	1.00[ASN][1000 genomes]
rs17152496	0.83[GIH][hapmap]
rs17152506	0.81[CHB][hapmap];0.82[GIH][hapmap]
rs17152525	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs17152543	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17152573	0.96[ASN][1000 genomes]
rs17152586	0.93[ASN][1000 genomes]
rs2069132	0.91[GIH][hapmap]
rs2079385	0.81[ASN][1000 genomes]
rs2107992	0.86[CHB][hapmap];0.87[GIH][hapmap]
rs2158707	0.86[CHB][hapmap];0.91[GIH][hapmap]
rs3884514	0.85[CHB][hapmap]
rs55817471	0.81[ASN][1000 genomes]
rs56169545	0.81[ASN][1000 genomes]
rs56234137	0.99[ASN][1000 genomes]
rs57335695	0.95[AFR][1000 genomes]
rs59968994	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60059862	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60262438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949250	0.94[ASN][1000 genomes]
rs6950987	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6953105	0.86[CHB][hapmap]
rs73149310	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73149323	0.96[ASN][1000 genomes]
rs73149326	0.96[ASN][1000 genomes]
rs73151318	0.81[ASN][1000 genomes]
rs73366517	0.99[AFR][1000 genomes]
rs7797165	0.90[GIH][hapmap]
rs7808217	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9640776	0.86[CHB][hapmap]
rs9641583	0.86[CHB][hapmap]
rs9641588	0.86[CHB][hapmap]
rs9641589	0.86[CHB][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs980354	ARL4C	trans	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79084400-79102200	Weak transcription	Left Ventricle	heart
2	chr7:79084600-79101000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:79084800-79100800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:79084800-79102800	Weak transcription	HSMM	muscle
5	chr7:79085000-79098600	Weak transcription	Fetal Muscle Leg	muscle
6	chr7:79085000-79099600	Weak transcription	Fetal Stomach	stomach
7	chr7:79085800-79095400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr7:79085800-79098000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:79086000-79099800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:79086600-79099600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:79086600-79100600	Weak transcription	Brain Anterior Caudate	brain
12	chr7:79086600-79101000	Weak transcription	Brain Angular Gyrus	brain
13	chr7:79086600-79101400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr7:79086600-79104200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr7:79087600-79099800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:79087800-79099800	Weak transcription	Fetal Lung	lung
17	chr7:79088000-79109600	Weak transcription	Aorta	Aorta
18	chr7:79089000-79098800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:79089000-79102800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:79089200-79098000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:79089200-79100200	Weak transcription	Adipose Nuclei	Adipose
22	chr7:79089200-79109600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:79089400-79101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:79089800-79099000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:79089800-79101800	Weak transcription	Liver	Liver
26	chr7:79090000-79101000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:79090200-79098600	Weak transcription	NHDF-Ad	bronchial
28	chr7:79091800-79101200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:79092000-79101800	Weak transcription	HUVEC	blood vessel
30	chr7:79092000-79103000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:79092200-79097800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:79092200-79097800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:79092200-79102200	Weak transcription	Ovary	ovary
34	chr7:79093800-79098000	Weak transcription	Brain Hippocampus Middle	brain
35	chr7:79094200-79097800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:79094200-79099800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:79094200-79099800	Weak transcription	Brain Substantia Nigra	brain
38	chr7:79094400-79099800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:79094600-79096800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:79094800-79097800	Weak transcription	NHLF	lung
41	chr7:79095200-79096200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr7:79095200-79097400	Weak transcription	Osteobl	bone

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