Variant report

Variant	rs798545
Chromosome Location	chr7:2762386-2762387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2760749..2763045-chr7:2764793..2766522,2	K562	blood:
2	chr7:2761837..2763894-chr7:2912353..2913943,2	MCF-7	breast:
3	chr7:2760677..2762584-chr7:2771267..2773265,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNA12-2	chr7:2762138-2762622	XLOC_006335

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs709282	0.87[ASN][1000 genomes]
rs798491	0.83[ASN][1000 genomes]
rs798492	0.87[ASN][1000 genomes]
rs798493	0.83[ASN][1000 genomes]
rs798494	0.83[ASN][1000 genomes]
rs798495	0.83[ASN][1000 genomes]
rs798497	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798498	0.87[ASN][1000 genomes]
rs798499	0.87[ASN][1000 genomes]
rs798500	0.84[ASN][1000 genomes]
rs798502	0.81[EUR][1000 genomes]
rs798508	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798511	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798512	0.89[ASN][1000 genomes]
rs798513	0.89[ASN][1000 genomes]
rs798514	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798518	0.86[ASN][1000 genomes]
rs798526	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798528	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798531	0.87[ASN][1000 genomes]
rs798536	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798540	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798544	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798546	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798547	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798548	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798550	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798551	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798552	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798554	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798555	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798556	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798557	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798558	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798559	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798560	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798562	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798563	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798565	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471227	chr7:2629020-2768864	Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv887309	chr7:2664214-2763102	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv887312	chr7:2707822-2763102	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1017611	chr7:2750418-2781716	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv538654	chr7:2750418-2781716	Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv971480	chr7:2755767-2765866	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs798545	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs798545	GNA12	cis	Artery Tibial	GTEx
rs798545	GNA12	cis	Nerve Tibial	GTEx
rs798545	GNA12	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2742200-2765600	Weak transcription	HSMM	muscle
2	chr7:2749400-2770600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:2749800-2770800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:2750000-2762800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:2750000-2765600	Weak transcription	Brain Substantia Nigra	brain
6	chr7:2750000-2767800	Weak transcription	Osteobl	bone
7	chr7:2750000-2768400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr7:2750000-2769000	Weak transcription	NHDF-Ad	bronchial
9	chr7:2750200-2765800	Weak transcription	Liver	Liver
10	chr7:2751000-2764400	Weak transcription	Brain Germinal Matrix	brain
11	chr7:2751200-2768400	Weak transcription	Brain Angular Gyrus	brain
12	chr7:2752400-2796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:2753400-2765800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr7:2753600-2768800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:2754600-2766800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:2754800-2774200	Weak transcription	Fetal Brain Male	brain
17	chr7:2755800-2770600	Weak transcription	Fetal Kidney	kidney
18	chr7:2756000-2777800	Weak transcription	Psoas Muscle	Psoas
19	chr7:2756200-2762800	Weak transcription	HSMMtube	muscle
20	chr7:2756200-2770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr7:2756400-2765600	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:2757200-2767400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:2757200-2770600	Weak transcription	Esophagus	oesophagus
24	chr7:2757400-2766200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:2757600-2772800	Weak transcription	Small Intestine	intestine
26	chr7:2757800-2763800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr7:2757800-2766800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:2757800-2768200	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:2757800-2768400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr7:2758000-2764600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr7:2758000-2765600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr7:2758000-2765800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:2758000-2768400	Weak transcription	HepG2	liver
34	chr7:2758000-2768600	Weak transcription	Right Atrium	heart
35	chr7:2758200-2762800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr7:2758200-2762800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:2758200-2762800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:2758200-2765400	Weak transcription	Colonic Mucosa	Colon
39	chr7:2758200-2766000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr7:2758200-2768000	Strong transcription	Fetal Stomach	stomach
41	chr7:2758200-2769400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr7:2758400-2762800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:2758400-2764600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:2758400-2765400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:2758400-2765800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:2758600-2762800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:2758600-2762800	Weak transcription	Dnd41	blood
48	chr7:2758600-2763000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:2758600-2765800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:2758600-2765800	Weak transcription	Duodenum Mucosa	Duodenum

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